From 09eb750fadadc429228eb2ae56d1233608d78ba2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 19:36:05 +0100
Subject: [PATCH 01/26] Don't pass around vue instance in rule builder

---
 .../components/RuleBuilder/RuleComponent.vue  |  5 +-
 .../RuleBuilder/RuleTargetComponent.vue       |  5 +-
 .../src/components/RuleCollectionBuilder.vue  | 83 +++++++++++--------
 3 files changed, 49 insertions(+), 44 deletions(-)

diff --git a/client/src/components/RuleBuilder/RuleComponent.vue b/client/src/components/RuleBuilder/RuleComponent.vue
index 4c69d0ef216f..6075393941ba 100644
--- a/client/src/components/RuleBuilder/RuleComponent.vue
+++ b/client/src/components/RuleBuilder/RuleComponent.vue
@@ -20,9 +20,6 @@ export default {
         displayRuleType: {
             required: true,
         },
-        builder: {
-            required: true,
-        },
     },
     data: function () {
         return {
@@ -40,7 +37,7 @@ export default {
             this.$emit("update:displayRuleType", null);
         },
         okay() {
-            this.builder.handleRuleSave(this.ruleType);
+            this.$emit("save-rule", this.ruleType);
             this.cancel();
         },
     },
diff --git a/client/src/components/RuleBuilder/RuleTargetComponent.vue b/client/src/components/RuleBuilder/RuleTargetComponent.vue
index 1dbd4f87fdf2..0e6b72dc6997 100644
--- a/client/src/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/src/components/RuleBuilder/RuleTargetComponent.vue
@@ -3,7 +3,7 @@
         class="rule-link dropdown-item"
         href="javascript:void(0)"
         :class="linkClassName"
-        @click="builder.addNewRule(ruleType)"
+        @click="$emit('add-new-rule', ruleType)"
         >{{ title }}</a
     >
 </template>
@@ -18,9 +18,6 @@ export default {
             type: String,
             required: true,
         },
-        builder: {
-            required: true,
-        },
     },
     computed: {
         linkClassName() {
diff --git a/client/src/components/RuleCollectionBuilder.vue b/client/src/components/RuleCollectionBuilder.vue
index d21c905d9f31..70a4c48479b7 100644
--- a/client/src/components/RuleCollectionBuilder.vue
+++ b/client/src/components/RuleCollectionBuilder.vue
@@ -51,7 +51,10 @@
                             'rules-container-horizontal': initialElements && horizontal,
                             'rules-container-full': initialElements == null,
                         }">
-                        <rule-component rule-type="sort" :display-rule-type.sync="displayRuleType" :builder="this">
+                        <rule-component
+                            rule-type="sort"
+                            :display-rule-type.sync="displayRuleType"
+                            @saveRule="handleRuleSave">
                             <column-selector :target.sync="addSortingTarget" :col-headers="activeRuleColHeaders" />
                             <label v-b-tooltip.hover :title="titleNumericSort">
                                 <input v-model="addSortingNumeric" type="checkbox" />
@@ -61,7 +64,7 @@
                         <rule-component
                             rule-type="add_column_basename"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="addColumnBasenameTarget"
                                 :col-headers="activeRuleColHeaders" />
@@ -69,7 +72,7 @@
                         <rule-component
                             rule-type="add_column_rownum"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <label>
                                 {{ l("Starting from") }}
                                 <input v-model="addColumnRownumStart" type="number" min="0" />
@@ -78,7 +81,7 @@
                         <rule-component
                             rule-type="add_column_metadata"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <label>
                                 {{ l("For") }}
                                 <select v-model="addColumnMetadataValue">
@@ -90,7 +93,7 @@
                         <rule-component
                             rule-type="add_column_group_tag_value"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <label>
                                 {{ l("Value") }}
                                 <input v-model="addColumnGroupTagValueValue" type="text" />
@@ -103,7 +106,7 @@
                         <rule-component
                             rule-type="add_column_regex"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector :target.sync="addColumnRegexTarget" :col-headers="activeRuleColHeaders" />
                             <label>
                                 <input v-model="addColumnRegexType" type="radio" value="global" />Create column matching
@@ -133,7 +136,7 @@
                         <rule-component
                             rule-type="add_column_concatenate"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="addColumnConcatenateTarget0"
                                 :col-headers="activeRuleColHeaders" />
@@ -144,7 +147,7 @@
                         <rule-component
                             rule-type="add_column_substr"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector :target.sync="addColumnSubstrTarget" :col-headers="activeRuleColHeaders" />
                             <label>
                                 <select v-model="addColumnSubstrType">
@@ -162,7 +165,7 @@
                         <rule-component
                             rule-type="add_column_value"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <label>
                                 {{ l("Value") }}
                                 <input v-model="addColumnValue" type="text" />
@@ -171,7 +174,7 @@
                         <rule-component
                             rule-type="remove_columns"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="removeColumnTargets"
                                 :col-headers="activeRuleColHeaders"
@@ -180,7 +183,7 @@
                         <rule-component
                             rule-type="split_columns"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="splitColumnsTargets0"
                                 label="Odd Row Column(s)"
@@ -195,7 +198,7 @@
                         <rule-component
                             rule-type="swap_columns"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="swapColumnsTarget0"
                                 label="Swap Column"
@@ -208,7 +211,7 @@
                         <rule-component
                             rule-type="add_filter_regex"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector :target.sync="addFilterRegexTarget" :col-headers="activeRuleColHeaders" />
                             <regular-expression-input :target.sync="addFilterRegexExpression" />
                             <label v-b-tooltip.hover :title="titleInvertFilterRegex">
@@ -219,7 +222,7 @@
                         <rule-component
                             rule-type="add_filter_matches"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="addFilterMatchesTarget"
                                 :col-headers="activeRuleColHeaders" />
@@ -232,7 +235,7 @@
                         <rule-component
                             rule-type="add_filter_compare"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector
                                 :target.sync="addFilterCompareTarget"
                                 :col-headers="activeRuleColHeaders" />
@@ -250,7 +253,7 @@
                         <rule-component
                             rule-type="add_filter_count"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <label>
                                 Filter which rows?
                                 <select v-model="addFilterCountWhich">
@@ -270,7 +273,7 @@
                         <rule-component
                             rule-type="add_filter_empty"
                             :display-rule-type.sync="displayRuleType"
-                            :builder="this">
+                            @saveRule="handleRuleSave">
                             <column-selector :target.sync="addFilterEmptyTarget" :col-headers="activeRuleColHeaders" />
                             <label v-b-tooltip.hover :title="titleInvertFilterEmpty">
                                 <input v-model="addFilterEmptyInvert" type="checkbox" />
@@ -384,10 +387,10 @@
                                         <span class="caret"></span>
                                     </button>
                                     <div class="dropdown-menu" role="menu">
-                                        <rule-target-component :builder="this" rule-type="sort" />
-                                        <rule-target-component :builder="this" rule-type="remove_columns" />
-                                        <rule-target-component :builder="this" rule-type="split_columns" />
-                                        <rule-target-component :builder="this" rule-type="swap_columns" />
+                                        <rule-target-component rule-type="sort" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="remove_columns" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="split_columns" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="swap_columns" @addNewRule="addNewRule" />
                                         <a
                                             href="javascript:void(0)"
                                             class="dropdown-item rule-link rule-link-mapping"
@@ -408,11 +411,15 @@
                                         <span class="caret"></span>
                                     </button>
                                     <div class="dropdown-menu" role="menu">
-                                        <rule-target-component :builder="this" rule-type="add_filter_regex" />
-                                        <rule-target-component :builder="this" rule-type="add_filter_matches" />
-                                        <rule-target-component :builder="this" rule-type="add_filter_compare" />
-                                        <rule-target-component :builder="this" rule-type="add_filter_empty" />
-                                        <rule-target-component :builder="this" rule-type="add_filter_count" />
+                                        <rule-target-component rule-type="add_filter_regex" @addNewRule="addNewRule" />
+                                        <rule-target-component
+                                            rule-type="add_filter_matches"
+                                            @addNewRule="addNewRule" />
+                                        <rule-target-component
+                                            rule-type="add_filter_compare"
+                                            @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_filter_empty" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_filter_count" @addNewRule="addNewRule" />
                                     </div>
                                 </div>
                                 <div class="dropup">
@@ -427,20 +434,24 @@
                                         <span class="caret"></span>
                                     </button>
                                     <div class="dropdown-menu" role="menu">
-                                        <rule-target-component :builder="this" rule-type="add_column_basename" />
+                                        <rule-target-component
+                                            rule-type="add_column_basename"
+                                            @addNewRule="addNewRule" />
                                         <rule-target-component
                                             v-if="metadataOptions"
-                                            :builder="this"
-                                            rule-type="add_column_metadata" />
+                                            rule-type="add_column_metadata"
+                                            @addNewRule="addNewRule" />
                                         <rule-target-component
                                             v-if="hasTagsMetadata"
-                                            :builder="this"
-                                            rule-type="add_column_group_tag_value" />
-                                        <rule-target-component :builder="this" rule-type="add_column_regex" />
-                                        <rule-target-component :builder="this" rule-type="add_column_concatenate" />
-                                        <rule-target-component :builder="this" rule-type="add_column_rownum" />
-                                        <rule-target-component :builder="this" rule-type="add_column_value" />
-                                        <rule-target-component :builder="this" rule-type="add_column_substr" />
+                                            rule-type="add_column_group_tag_value"
+                                            @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_column_regex" @addNewRule="addNewRule" />
+                                        <rule-target-component
+                                            rule-type="add_column_concatenate"
+                                            @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_column_rownum" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_column_value" @addNewRule="addNewRule" />
+                                        <rule-target-component rule-type="add_column_substr" @addNewRule="addNewRule" />
                                     </div>
                                 </div>
                             </div>

From 42fe9c339385bf1094d4148debfd563fc7593ba2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 19:36:53 +0100
Subject: [PATCH 02/26] Don't add user-id to local storage key for saved rules

---
 .../src/components/RuleBuilder/SaveRules.vue  | 37 +++++++++----------
 1 file changed, 17 insertions(+), 20 deletions(-)

diff --git a/client/src/components/RuleBuilder/SaveRules.vue b/client/src/components/RuleBuilder/SaveRules.vue
index af71ef5db581..01107e54539f 100644
--- a/client/src/components/RuleBuilder/SaveRules.vue
+++ b/client/src/components/RuleBuilder/SaveRules.vue
@@ -1,15 +1,12 @@
 <script>
-import { getGalaxyInstance } from "app";
+const NO_SECOND_ISO_DATE_REGEX = /\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d/;
+
 export default {
     props: {
         prefix: {
             type: String,
             default: "galaxy_rules_",
         },
-        user: {
-            type: String,
-            default: getGalaxyInstance() ? getGalaxyInstance().user.id : "",
-        },
     },
     data: function () {
         return {
@@ -18,23 +15,23 @@ export default {
     },
     created() {
         let counter = 0;
-        if (this.user == null) {
-            return;
-        } else {
-            for (let i = 0; i < localStorage.length; i++) {
-                if (localStorage.key(i).startsWith(this.prefix + this.user)) {
-                    var savedSession = localStorage.getItem(localStorage.key(i));
-                    if (savedSession) {
-                        var key = localStorage.key(i);
+        for (let i = 0; i < localStorage.length; i++) {
+            if (localStorage.key(i).startsWith(this.prefix)) {
+                const rule = localStorage.getItem(localStorage.key(i));
+                if (rule) {
+                    const key = localStorage.key(i);
+                    const dateMatch = key.match(NO_SECOND_ISO_DATE_REGEX);
+                    if (dateMatch) {
+                        const dateTime = key.slice(dateMatch.index);
                         this.savedRules.push({
-                            dateTime: key.substring(this.prefix.length + this.user.length),
-                            rule: savedSession,
+                            dateTime,
+                            rule,
                         });
+                        counter++;
                     }
-                    counter++;
-                    if (counter == 10) {
-                        break;
-                    }
+                }
+                if (counter == 10) {
+                    break;
                 }
             }
         }
@@ -42,7 +39,7 @@ export default {
     methods: {
         saveSession(jsonRulesString) {
             var dateTimeString = new Date().toISOString();
-            var key = this.prefix + this.user + dateTimeString;
+            var key = this.prefix + dateTimeString;
             localStorage.setItem(key, jsonRulesString);
             this.savedRules.push({
                 dateTime: dateTimeString,

From 8deac11e321f1146f72eafc75a995cb6e770fd19 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 19:32:05 +0100
Subject: [PATCH 03/26] Fix rule builder table not rendering until user clicks,
 scrolls or resizes

---
 client/src/components/RuleCollectionBuilder.vue | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/client/src/components/RuleCollectionBuilder.vue b/client/src/components/RuleCollectionBuilder.vue
index 70a4c48479b7..521677aa40ad 100644
--- a/client/src/components/RuleCollectionBuilder.vue
+++ b/client/src/components/RuleCollectionBuilder.vue
@@ -1212,6 +1212,13 @@ export default {
                 });
         }
     },
+    mounted() {
+        // something bizarre is up with the rendering of hands-on-table, needs a click to render.
+        // Vue.nextTick() didn't work here.
+        setTimeout(() => {
+            this.$refs.hotTable.$el.click();
+        }, 200);
+    },
     methods: {
         restoreRules(event) {
             const json = JSON.parse(event);

From c76a48b6c8f31747c3f990b927c863900baa0b4f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Mar 2023 20:20:27 +0100
Subject: [PATCH 04/26] Drop var

---
 client/src/components/RuleBuilder/SaveRules.vue | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/client/src/components/RuleBuilder/SaveRules.vue b/client/src/components/RuleBuilder/SaveRules.vue
index 01107e54539f..f6a70321cb70 100644
--- a/client/src/components/RuleBuilder/SaveRules.vue
+++ b/client/src/components/RuleBuilder/SaveRules.vue
@@ -37,13 +37,13 @@ export default {
         }
     },
     methods: {
-        saveSession(jsonRulesString) {
-            var dateTimeString = new Date().toISOString();
-            var key = this.prefix + dateTimeString;
-            localStorage.setItem(key, jsonRulesString);
+        saveSession(rule) {
+            const dateTime = new Date().toISOString();
+            const key = this.prefix + dateTime;
+            localStorage.setItem(key, rule);
             this.savedRules.push({
-                dateTime: dateTimeString,
-                rule: jsonRulesString,
+                dateTime,
+                rule,
             });
         },
     },

From 054d2c71a2bba7ac7d56fbc1fcd98c9f8f00b85e Mon Sep 17 00:00:00 2001
From: Patrick Austin <patrick.austin@stfc.ac.uk>
Date: Tue, 14 Mar 2023 15:38:41 +0000
Subject: [PATCH 05/26] Account for charge and spin in den_fmt sniffer

---
 lib/galaxy/datatypes/test/YbCuAs2.den_fmt | 13 +++++++++++++
 lib/galaxy/datatypes/text.py              | 10 +++++++++-
 2 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy/datatypes/test/YbCuAs2.den_fmt

diff --git a/lib/galaxy/datatypes/test/YbCuAs2.den_fmt b/lib/galaxy/datatypes/test/YbCuAs2.den_fmt
new file mode 100644
index 000000000000..5bd6ea7a9121
--- /dev/null
+++ b/lib/galaxy/datatypes/test/YbCuAs2.den_fmt
@@ -0,0 +1,13 @@
+ BEGIN header
+  
+           Real Lattice(A)               Lattice parameters(A)    Cell Angles
+     3.8420000     0.0000000     0.0000000     a =    3.842000  alpha =   90.000000
+     0.0000000     3.8420000     0.0000000     b =    3.842000  beta  =   90.000000
+     0.0000000     0.0000000     9.7430000     c =    9.743000  gamma =   90.000000
+  
+   2                            ! nspins
+  32    32    90                ! fine FFT grid along <a,b,c>
+ END header: data is "<a b c> charge spin" in units of electrons/grid_point * nu
+ mber of grid_points
+  
+     1     1     1           47.798968            0.000070
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 9ffa741f327e..42f555dbba3b 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -1188,6 +1188,9 @@ def sniff_prefix(self, file_prefix: FilePrefix):
         >>> fname = get_test_fname('Si.den_fmt')
         >>> FormattedDensity().sniff(fname)
         True
+        >>> fname = get_test_fname('YbCuAs2.den_fmt')
+        >>> FormattedDensity().sniff(fname)
+        True
         >>> fname = get_test_fname('Si.param')
         >>> FormattedDensity().sniff(fname)
         False
@@ -1195,6 +1198,11 @@ def sniff_prefix(self, file_prefix: FilePrefix):
         begin_header = "BEGIN header"
         end_header = 'END header: data is "<a b c> charge" in units of electrons/grid_point * number'
         grid_points = "of grid_points"
+        end_header_spin = 'END header: data is "<a b c> charge spin" in units of electrons/grid_point * nu'
+        grid_points_spin = "mber of grid_points"
         handle = file_prefix.string_io()
         lines = handle.readlines()
-        return lines[0].strip() == begin_header and lines[9].strip() == end_header and lines[10].strip() == grid_points
+        return lines[0].strip() == begin_header and (
+            (lines[9].strip() == end_header and lines[10].strip() == grid_points)
+            or (lines[9].strip() == end_header_spin and lines[10].strip() == grid_points_spin)
+        )

From 32b7ef9572682cfe97bf4db527fad72e33a5c5e2 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <newadmin@galaxyc.local>
Date: Tue, 14 Mar 2023 16:40:23 -0400
Subject: [PATCH 06/26] Fix loading of job submission success page on route
 change

---
 client/src/components/Tool/ToolForm.vue | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index ff43958cb5a1..236abdfc70a6 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -316,9 +316,11 @@ export default {
                 jobDef.inputs["use_cached_job"] = true;
             }
             console.debug("toolForm::onExecute()", jobDef);
+            const prevRoute = this.$route.fullPath;
             submitJob(jobDef).then(
                 (jobResponse) => {
                     this.showExecuting = false;
+                    let changeRoute = false;
                     refreshContentsWrapper();
                     if (jobResponse.produces_entry_points) {
                         this.showEntryPoints = true;
@@ -335,17 +337,21 @@ export default {
                             toolName: this.toolName,
                         };
                         this.saveLatestResponse(response);
-                        this.$router.push(`/jobs/submission/success`);
+                        changeRoute = prevRoute === this.$route.fullPath;
                     } else {
                         this.showError = true;
                         this.showForm = true;
                         this.errorTitle = "Job submission rejected.";
                         this.errorContent = jobResponse;
                     }
-                    if ([true, "true"].includes(config.enable_tool_recommendations)) {
-                        this.showRecommendation = true;
+                    if (changeRoute) {
+                        this.$router.push(`/jobs/submission/success`);
+                    } else {
+                        if ([true, "true"].includes(config.enable_tool_recommendations)) {
+                            this.showRecommendation = true;
+                        }
+                        document.querySelector(".center-panel").scrollTop = 0;
                     }
-                    document.querySelector(".center-panel").scrollTop = 0;
                 },
                 (e) => {
                     this.errorMessage = e?.response?.data?.err_msg;

From 3b93982e3454bd49066f0007d93c1aefe7a7a5f0 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 15 Mar 2023 17:09:48 +0300
Subject: [PATCH 07/26] Display workflow error messages in markdown pages

---
 .../Elements/Workflow/WorkflowDisplay.vue     | 30 ++++++++++++++-----
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
index 2bcdcb804469..18a16b1bbd25 100644
--- a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
+++ b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
@@ -34,9 +34,19 @@
         <b-card-body>
             <LoadingSpan v-if="loading" message="Loading Workflow" />
             <div v-else :class="!expanded && 'content-height'">
-                <div v-for="step in itemContent.steps" :key="step.order_index" class="mb-2">
-                    <div>Step {{ step.order_index + 1 }}: {{ step.label }}</div>
-                    <WorkflowTree :input="step" :skip-head="true" />
+                <b-alert v-if="errorDict" variant="danger" show>
+                    <b>Please fix the following error(s):</b>
+                    <ul class="my-2">
+                        <li v-for="(errorValue, errorKey) in errorDict" :key="errorKey">
+                            {{ errorKey }}: {{ errorValue }}
+                        </li>
+                    </ul>
+                </b-alert>
+                <div v-else>
+                    <div v-for="step in itemContent.steps" :key="step.order_index" class="mb-2">
+                        <div>Step {{ step.order_index + 1 }}: {{ step.label }}</div>
+                        <WorkflowTree :input="step" :skip-head="true" />
+                    </div>
                 </div>
             </div>
         </b-card-body>
@@ -69,6 +79,7 @@ export default {
     },
     data() {
         return {
+            errorDict: null,
             itemContent: null,
             loading: true,
         };
@@ -89,10 +100,15 @@ export default {
     },
     created() {
         const url = this.itemUrl;
-        urlData({ url }).then((data) => {
-            this.itemContent = data;
-            this.loading = false;
-        });
+        urlData({ url })
+            .then((data) => {
+                this.itemContent = data;
+                this.loading = false;
+            })
+            .catch((errorDict) => {
+                this.errorDict = errorDict;
+                this.loading = false;
+            });
     },
 };
 </script>

From a7709fd8cfab608b7aa5a99760e5df6d6dd13b04 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 15 Mar 2023 17:28:32 +0300
Subject: [PATCH 08/26] Add workflow element markdown test for error case

---
 .../Elements/Workflow/WorkflowDisplay.test.js | 69 ++++++++++++++-----
 1 file changed, 50 insertions(+), 19 deletions(-)

diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
index 2cf1191a8879..d04ab7533472 100644
--- a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
+++ b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
@@ -1,4 +1,5 @@
 import axios from "axios";
+import flushPromises from "flush-promises";
 import MockAdapter from "axios-mock-adapter";
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
@@ -6,33 +7,53 @@ import MountTarget from "./WorkflowDisplay";
 
 const localVue = getLocalVue(true);
 
-describe("WorkflowDisplay", () => {
-    let wrapper;
-    let axiosMock;
+let axiosMock;
 
-    beforeEach(() => {
-        axiosMock = new MockAdapter(axios);
-        const data = {};
-        axiosMock.onGet(`/api/workflows/workflow_id/download?style=preview`).reply(200, data);
-        wrapper = mount(MountTarget, {
-            propsData: {
-                args: {
-                    workflow_id: "workflow_id",
-                },
-                embedded: false,
-                expanded: false,
+function mountDefault() {
+    axiosMock = new MockAdapter(axios);
+    const data = {
+        name: "workflow_name",
+    };
+    axiosMock.onGet(`/api/workflows/workflow_id/download?style=preview`).reply(200, data);
+    return mount(MountTarget, {
+        propsData: {
+            args: {
+                workflow_id: "workflow_id",
             },
-            localVue,
-        });
+            embedded: false,
+            expanded: false,
+        },
+        localVue,
     });
+}
 
-    afterEach(() => {
-        axiosMock.reset();
+function mountError() {
+    axiosMock = new MockAdapter(axios);
+    const data = {
+        err_msg: {
+            firstError: "firstValue",
+            secondError: "secondValue",
+        },
+    };
+    axiosMock.onGet(`/api/workflows/workflow_id/download?style=preview`).reply(400, data);
+    return mount(MountTarget, {
+        propsData: {
+            args: {
+                workflow_id: "workflow_id",
+            },
+            embedded: false,
+            expanded: false,
+        },
+        localVue,
     });
+}
 
+describe("WorkflowDisplay", () => {
     it("basics", async () => {
+        const wrapper = mountDefault();
+        await flushPromises();
         const cardHeader = wrapper.find(".card-header");
-        expect(cardHeader.text()).toBe("Workflow:");
+        expect(cardHeader.text()).toBe("Workflow: workflow_name");
         const downloadUrl = wrapper.find("[data-description='workflow download']");
         expect(downloadUrl.attributes("href")).toBe("/api/workflows/workflow_id/download?format=json-download");
         const importUrl = wrapper.find("[data-description='workflow import']");
@@ -40,4 +61,14 @@ describe("WorkflowDisplay", () => {
         const dataRequest = axiosMock.history.get[0].url;
         expect(dataRequest).toBe("/api/workflows/workflow_id/download?style=preview");
     });
+
+    it("error messages", async () => {
+        const wrapper = mountError();
+        await flushPromises();
+        const cardHeader = wrapper.find(".card-header");
+        expect(cardHeader.text()).toBe("Workflow: ...");
+        const errorMessages = wrapper.findAll("li");
+        expect(errorMessages.at(0).text()).toBe("firstError: firstValue");
+        expect(errorMessages.at(1).text()).toBe("secondError: secondValue");
+    });
 });

From bb1077d84db33589607db39b61a8dcc805c4909c Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Wed, 15 Mar 2023 18:40:15 +0300
Subject: [PATCH 09/26] Handle errors returned as simple strings instead of
 objects or arrays

---
 .../Elements/Workflow/WorkflowDisplay.test.js | 27 ++++++++++++-------
 .../Elements/Workflow/WorkflowDisplay.vue     | 13 ++++-----
 2 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
index d04ab7533472..85a78fc1a616 100644
--- a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
+++ b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.test.js
@@ -27,13 +27,10 @@ function mountDefault() {
     });
 }
 
-function mountError() {
+function mountError(errContent) {
     axiosMock = new MockAdapter(axios);
     const data = {
-        err_msg: {
-            firstError: "firstValue",
-            secondError: "secondValue",
-        },
+        err_msg: errContent,
     };
     axiosMock.onGet(`/api/workflows/workflow_id/download?style=preview`).reply(400, data);
     return mount(MountTarget, {
@@ -62,13 +59,23 @@ describe("WorkflowDisplay", () => {
         expect(dataRequest).toBe("/api/workflows/workflow_id/download?style=preview");
     });
 
-    it("error messages", async () => {
-        const wrapper = mountError();
+    it("error message as object", async () => {
+        const wrapper = mountError({
+            firstError: "firstValue",
+            secondError: "secondValue",
+        });
         await flushPromises();
         const cardHeader = wrapper.find(".card-header");
         expect(cardHeader.text()).toBe("Workflow: ...");
-        const errorMessages = wrapper.findAll("li");
-        expect(errorMessages.at(0).text()).toBe("firstError: firstValue");
-        expect(errorMessages.at(1).text()).toBe("secondError: secondValue");
+        const errorContent = wrapper.findAll("li");
+        expect(errorContent.at(0).text()).toBe("firstError: firstValue");
+        expect(errorContent.at(1).text()).toBe("secondError: secondValue");
+    });
+
+    it("error message as text", async () => {
+        const wrapper = mountError("Something went wrong.");
+        await flushPromises();
+        const errorContent = wrapper.find(".alert > div");
+        expect(errorContent.text()).toBe("Something went wrong.");
     });
 });
diff --git a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
index 18a16b1bbd25..725c30db0e0c 100644
--- a/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
+++ b/client/src/components/Markdown/Elements/Workflow/WorkflowDisplay.vue
@@ -34,13 +34,14 @@
         <b-card-body>
             <LoadingSpan v-if="loading" message="Loading Workflow" />
             <div v-else :class="!expanded && 'content-height'">
-                <b-alert v-if="errorDict" variant="danger" show>
+                <b-alert v-if="errorContent" variant="danger" show>
                     <b>Please fix the following error(s):</b>
-                    <ul class="my-2">
-                        <li v-for="(errorValue, errorKey) in errorDict" :key="errorKey">
+                    <ul v-if="typeof errorContent === 'object'" class="my-2">
+                        <li v-for="(errorValue, errorKey) in errorContent" :key="errorKey">
                             {{ errorKey }}: {{ errorValue }}
                         </li>
                     </ul>
+                    <div v-else>{{ errorContent }}</div>
                 </b-alert>
                 <div v-else>
                     <div v-for="step in itemContent.steps" :key="step.order_index" class="mb-2">
@@ -79,7 +80,7 @@ export default {
     },
     data() {
         return {
-            errorDict: null,
+            errorContent: null,
             itemContent: null,
             loading: true,
         };
@@ -105,8 +106,8 @@ export default {
                 this.itemContent = data;
                 this.loading = false;
             })
-            .catch((errorDict) => {
-                this.errorDict = errorDict;
+            .catch((errorContent) => {
+                this.errorContent = errorContent;
                 this.loading = false;
             });
     },

From aa2b4158719a014f6d816425a8107a9c54f878c3 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 15 Mar 2023 14:39:12 -0400
Subject: [PATCH 10/26] Swap history dataset counter icons to toggle and clear
 filter on a second click

---
 .../History/CurrentHistory/HistoryCounter.vue   | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/client/src/components/History/CurrentHistory/HistoryCounter.vue b/client/src/components/History/CurrentHistory/HistoryCounter.vue
index d73e626733e8..9e0f25105d00 100644
--- a/client/src/components/History/CurrentHistory/HistoryCounter.vue
+++ b/client/src/components/History/CurrentHistory/HistoryCounter.vue
@@ -28,7 +28,7 @@
                 variant="link"
                 size="sm"
                 class="rounded-0 text-decoration-none"
-                @click="setFilter('deleted:true')">
+                @click="toggleDeleted()">
                 <icon icon="trash" />
                 <span>{{ numItemsDeleted }}</span>
             </b-button>
@@ -72,6 +72,7 @@ export default {
         history: { type: Object, required: true },
         isWatching: { type: Boolean, default: false },
         lastChecked: { type: Date, default: null },
+        filterText: { type: String, default: "" },
     },
     data() {
         return {
@@ -92,6 +93,20 @@ export default {
         setFilter(newFilterText) {
             this.$emit("update:filter-text", newFilterText);
         },
+        toggleDeleted() {
+            if (this.filterText === "deleted:true") {
+                this.setFilter("");
+            } else {
+                this.setFilter("deleted:true");
+            }
+        },
+        toggleHidden() {
+            if (this.filterText === "visible:false") {
+                this.setFilter("");
+            } else {
+                this.setFilter("visible:false");
+            }
+        },
         updateTime() {
             const diffToNow = formatDistanceToNowStrict(this.lastChecked, { addSuffix: true, includeSeconds: true });
             const diffToNowSec = Date.now() - this.lastChecked;

From dfe671400b296ccc1aa38e7420ed65636c6abf07 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 15 Mar 2023 22:02:54 +0100
Subject: [PATCH 11/26] Fix toggling output visibility

---
 client/src/components/Workflow/Editor/NodeOutput.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/Workflow/Editor/NodeOutput.vue b/client/src/components/Workflow/Editor/NodeOutput.vue
index 1231b7117281..bb5001116887 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.vue
+++ b/client/src/components/Workflow/Editor/NodeOutput.vue
@@ -120,7 +120,7 @@ function onToggleActive() {
 
 function onToggleVisible() {
     const actionKey = `HideDatasetAction${props.output.name}`;
-    const step = stepStore.getStep(stepId.value);
+    const step = { ...stepStore.getStep(stepId.value) };
     if (isVisible.value) {
         step.post_job_actions = {
             ...step.post_job_actions,

From 66bf2c7d1f7f87c46078862c5cc99d9e9dde5d00 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Thu, 16 Mar 2023 05:56:42 +0300
Subject: [PATCH 12/26] Properly display missing tools in subworkflows instead
 of throwing generic error

---
 lib/galaxy/workflow/modules.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index a95f8140bc5e..1ec0afef118d 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -805,7 +805,8 @@ def get_runtime_inputs(self, connections=None):
             if step.type == "tool":
                 assert isinstance(step.module, ToolModule)
                 tool = step.module.tool
-                assert tool
+                if tool is None:
+                    raise ToolMissingException("Tool in subworkflow missing.", tool_id=step.module.tool_id)
                 tool_inputs = step.module.state
 
                 def callback(input, prefixed_name, prefixed_label, value=None, **kwds):

From da0427b73af8dd0468cc96e6e8ee19827e0212b6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 16 Mar 2023 12:32:06 +0100
Subject: [PATCH 13/26] Fix overly strict map over constraints

---
 .../Workflow/Editor/modules/terminals.test.ts | 23 ++++++++++---------
 .../Workflow/Editor/modules/terminals.ts      |  2 +-
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index 10936b48b4b5..18b88acbc9c5 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -385,16 +385,13 @@ describe("canAccept", () => {
         expect(collectionIn.canAccept(pairedOut).canAccept).toBe(false);
         expect(collectionIn.canAccept(pairedOut).reason).toBe("Incompatible collection type(s) for attachment.");
     });
-    it("rejects mapping over collection input if other inputs have an incompatible map over collection type", () => {
+    it("accepts a collection input if other input has a map over collection type", () => {
         const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
         const listListOut = terminals["list:list input"]["output"] as OutputCollectionTerminal;
         const listOneIn = terminals["two list inputs"]["kind|f1"] as InputCollectionTerminal;
         const listTwoIn = terminals["two list inputs"]["kind|f2"] as InputCollectionTerminal;
         listOneIn.connect(listListOut);
-        expect(listTwoIn.canAccept(collectionOut).canAccept).toBe(false);
-        expect(listTwoIn.canAccept(collectionOut).reason).toBe(
-            "Can't map over this input with output collection type - other inputs have an incompatible map over collection type. Disconnect inputs (and potentially outputs) and retry."
-        );
+        expect(listTwoIn.canAccept(collectionOut).canAccept).toBe(true);
     });
     it("rejects mapping over collection input if outputs constrain input to incompatible collection type", () => {
         const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
@@ -404,11 +401,15 @@ describe("canAccept", () => {
         const mapOverOut = terminals["two list inputs"]["out1"] as OutputTerminal;
         const dataIn = terminals["simple data"]["input"] as InputTerminal;
         listOneIn.connect(listListOut);
+        // two list inputs constrained to a list map over
         dataIn.connect(mapOverOut);
         listOneIn.disconnect(listListOut);
-        // TODO: this should be possible eventually IMHO
-        expect(listTwoIn.canAccept(collectionOut).canAccept).toBe(false);
-        expect(listTwoIn.canAccept(collectionOut).reason).toBe(
+        // still constrained to list map over via output connection
+        // can accept other input
+        expect(listTwoIn.canAccept(collectionOut).canAccept).toBe(true);
+        // but cannot accept on the constrained input
+        expect(listOneIn.canAccept(collectionOut).canAccept).toBe(false);
+        expect(listOneIn.canAccept(collectionOut).reason).toBe(
             "Can't map over this input with output collection type - this step has outputs defined constraining the mapping of this tool. Disconnect outputs and retry."
         );
     });
@@ -462,7 +463,7 @@ describe("canAccept", () => {
         );
     });
     it("rejects connections to input collection constrained by other input", () => {
-        const collectionOut = terminals["list input"]["output"] as OutputCollectionTerminal;
+        const listListListOut = terminals["list:list:list input"]["output"] as OutputCollectionTerminal;
         const dataIn = terminals["simple data"]["input"] as InputTerminal;
         const listOneIn = terminals["two list inputs"]["kind|f1"] as InputCollectionTerminal;
         const listTwoIn = terminals["two list inputs"]["kind|f2"] as InputCollectionTerminal;
@@ -472,8 +473,8 @@ describe("canAccept", () => {
         listOneIn.connect(listListOut);
         dataIn.connect(mapOverOut);
         // Can't connect list as output acts like "list:list"
-        expect(listTwoIn.canAccept(collectionOut).canAccept).toBe(false);
-        expect(listTwoIn.canAccept(collectionOut).reason).toBe(
+        expect(listTwoIn.canAccept(listListListOut).canAccept).toBe(false);
+        expect(listTwoIn.canAccept(listListListOut).reason).toBe(
             "Can't map over this input with output collection type - other inputs have an incompatible map over collection type. Disconnect inputs (and potentially outputs) and retry."
         );
     });
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index fe58c4b6dbc9..bfb95e0ca38f 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -540,7 +540,7 @@ export class InputCollectionTerminal extends BaseInputTerminal {
         return NULL_COLLECTION_TYPE_DESCRIPTION;
     }
     _effectiveCollectionTypes() {
-        return this.collectionTypes.map((t) => this.mapOver.append(t));
+        return this.collectionTypes.map((t) => this.localMapOver.append(t));
     }
     attachable(other: BaseOutputTerminal) {
         const otherCollectionType = this._otherCollectionType(other);

From 85cf9735a659160ffec4b43582c5f75365a08695 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 17 Mar 2023 10:50:33 -0400
Subject: [PATCH 14/26] Add eof newline to den_fmt test data

---
 lib/galaxy/datatypes/test/YbCuAs2.den_fmt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/test/YbCuAs2.den_fmt b/lib/galaxy/datatypes/test/YbCuAs2.den_fmt
index 5bd6ea7a9121..febd3b420251 100644
--- a/lib/galaxy/datatypes/test/YbCuAs2.den_fmt
+++ b/lib/galaxy/datatypes/test/YbCuAs2.den_fmt
@@ -10,4 +10,5 @@
  END header: data is "<a b c> charge spin" in units of electrons/grid_point * nu
  mber of grid_points
   
-     1     1     1           47.798968            0.000070
\ No newline at end of file
+     1     1     1           47.798968            0.000070
+

From 2b99b2752a62b23bda2d9458c00267040a4f94be Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Fri, 17 Mar 2023 20:26:57 +0100
Subject: [PATCH 15/26] Use camelCase for emitted events

Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com>
---
 client/src/components/RuleBuilder/RuleComponent.vue       | 2 +-
 client/src/components/RuleBuilder/RuleTargetComponent.vue | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/components/RuleBuilder/RuleComponent.vue b/client/src/components/RuleBuilder/RuleComponent.vue
index 6075393941ba..b2d83eba3f64 100644
--- a/client/src/components/RuleBuilder/RuleComponent.vue
+++ b/client/src/components/RuleBuilder/RuleComponent.vue
@@ -37,7 +37,7 @@ export default {
             this.$emit("update:displayRuleType", null);
         },
         okay() {
-            this.$emit("save-rule", this.ruleType);
+            this.$emit("saveRule", this.ruleType);
             this.cancel();
         },
     },
diff --git a/client/src/components/RuleBuilder/RuleTargetComponent.vue b/client/src/components/RuleBuilder/RuleTargetComponent.vue
index 0e6b72dc6997..d2eb57fa0102 100644
--- a/client/src/components/RuleBuilder/RuleTargetComponent.vue
+++ b/client/src/components/RuleBuilder/RuleTargetComponent.vue
@@ -3,7 +3,7 @@
         class="rule-link dropdown-item"
         href="javascript:void(0)"
         :class="linkClassName"
-        @click="$emit('add-new-rule', ruleType)"
+        @click="$emit('addNewRule', ruleType)"
         >{{ title }}</a
     >
 </template>

From 6afcbe29c335c15296ae2c3655feb626ffe27d40 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 16 Mar 2023 11:42:10 +0100
Subject: [PATCH 16/26] Display confirmation dialog when attepmting to save
 workflow with invalid connections

Closes https://github.com/galaxyproject/galaxy/issues/15753
---
 .../components/Workflow/Editor/Options.vue    | 77 +++++++++++++------
 client/src/utils/navigation/navigation.yml    |  1 +
 .../selenium/test_workflow_editor.py          |  8 +-
 3 files changed, 59 insertions(+), 27 deletions(-)

diff --git a/client/src/components/Workflow/Editor/Options.vue b/client/src/components/Workflow/Editor/Options.vue
index e5e342930dc6..8ce5effe8ea5 100644
--- a/client/src/components/Workflow/Editor/Options.vue
+++ b/client/src/components/Workflow/Editor/Options.vue
@@ -1,3 +1,55 @@
+<script setup lang="ts">
+import { computed } from "vue";
+import { BDropdown, BDropdownItem, BButton } from "bootstrap-vue";
+import { useConfirmDialog } from "@/composables/confirmDialog";
+
+const emit = defineEmits<{
+    (e: "onAttributes"): void;
+    (e: "onSave"): void;
+    (e: "onReport"): void;
+    (e: "onSaveAs"): void;
+    (e: "onLayout"): void;
+    (e: "onUpgrade"): void;
+    (e: "onDownload"): void;
+    (e: "onRun"): void;
+}>();
+
+const props = defineProps<{
+    hasChanges?: boolean;
+    hasInvalidConnections?: boolean;
+    requiredReindex?: boolean;
+}>();
+
+const { confirm } = useConfirmDialog();
+
+const saveHover = computed(() => {
+    if (!props.hasChanges) {
+        return "Workflow has no changes";
+    } else if (props.hasInvalidConnections) {
+        return "Workflow has invalid connections, review and remove invalid connections";
+    } else {
+        return "Save Workflow";
+    }
+});
+
+async function onSave() {
+    if (props.hasInvalidConnections) {
+        console.log("getting confirmation");
+        const confirmed = await confirm(
+            `Workflow has invalid connections. You can save the workflow, but it may not run correctly.`,
+            {
+                id: "save-workflow-confirmation",
+                okTitle: "Save Workflow",
+            }
+        );
+        if (confirmed) {
+            emit("onSave");
+        }
+    } else {
+        emit("onSave");
+    }
+}
+</script>
 <template>
     <div class="panel-header-buttons">
         <b-button
@@ -18,8 +70,8 @@
                 variant="link"
                 aria-label="Save Workflow"
                 class="editor-button-save"
-                :disabled="!hasChanges || hasInvalidConnections"
-                @click="$emit('onSave')">
+                :disabled="!hasChanges"
+                @click="onSave">
                 <span class="fa fa-floppy-o" />
             </b-button>
         </b-button-group>
@@ -76,24 +128,3 @@
         </b-button>
     </div>
 </template>
-
-<script setup lang="ts">
-import { computed } from "vue";
-import { BDropdown, BDropdownItem, BButton } from "bootstrap-vue";
-
-const props = defineProps<{
-    hasChanges?: boolean;
-    hasInvalidConnections?: boolean;
-    requiredReindex?: boolean;
-}>();
-
-const saveHover = computed(() => {
-    if (!props.hasChanges) {
-        return "Workflow has no changes";
-    } else if (props.hasInvalidConnections) {
-        return "Workflow has invalid connections, review and remove invalid connections";
-    } else {
-        return "Save Workflow";
-    }
-});
-</script>
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index f97006e4b7a5..99baf126c23a 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -665,6 +665,7 @@ workflow_editor:
     connector_invalid_for: "#connection-${sink_id}-${source_id} .ribbon-inner-invalid"
     connector_destroy_callout: '.delete-terminal'
     save_button: '.editor-button-save'
+    save_workflow_confirmation_button: '#save-workflow-confirmation .btn-primary'
     state_modal_body: '.state-upgrade-modal'
     modal_button_continue: '.modal-footer .btn'
 
diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
index e6fb6bae8936..27935713507c 100644
--- a/lib/galaxy_test/selenium/test_workflow_editor.py
+++ b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -557,17 +557,17 @@ def test_change_datatype(self):
         editor.select_datatype(datatype="bam").wait_for_and_click()
         editor.node.output_data_row(output_name="out_file1", extension="bam").wait_for_visible()
         self.assert_connection_invalid("create_2#out_file1", "checksum#input")
+        # Assert save button
         save_button = self.components.workflow_editor.save_button
-        # Assert save button is disabled
-        assert save_button.has_class("disabled")
+        save_button.wait_for_and_click()
+        # Will trigger confirmation modal
+        self.components.workflow_editor.save_workflow_confirmation_button.wait_for_and_click()
         # Make connection valid again
         editor.change_datatype.wait_for_and_click()
         editor.select_datatype_text_search.wait_for_and_send_keys("tabular")
         editor.select_datatype(datatype="tabular").wait_for_and_click()
         # Assert connection is valid
         self.assert_connected("create_2#out_file1", "checksum#input")
-        # Assert save button is enabled
-        assert not save_button.has_class("disabled")
 
     @selenium_test
     def test_change_datatype_post_job_action_lost_regression(self):

From 6718308d9e5571e902e177a958241eb0fd9d9582 Mon Sep 17 00:00:00 2001
From: Ahmed Awan <qe66653@umbc.edu>
Date: Fri, 17 Mar 2023 16:04:28 -0400
Subject: [PATCH 17/26] Fix User Preferences Manage External Identities element
 v-if

---
 client/src/components/User/UserPreferences.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/User/UserPreferences.vue b/client/src/components/User/UserPreferences.vue
index 09afa1e0532f..f12a57ebb690 100644
--- a/client/src/components/User/UserPreferences.vue
+++ b/client/src/components/User/UserPreferences.vue
@@ -43,7 +43,7 @@
             to="/user/cloud_auth" />
         <ConfigProvider v-slot="{ config }">
             <user-preferences-element
-                v-if="!config.enable_oidc"
+                v-if="config.enable_oidc"
                 id="manage-third-party-identities"
                 icon="fa-id-card-o"
                 title="Manage Third-Party Identities"

From bfc5baad88db13ee96bcc3e409e12874b230c8f9 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Sat, 18 Mar 2023 11:08:42 +0100
Subject: [PATCH 18/26] Add missing onLint event

Co-authored-by: Dannon <dannon.baker@gmail.com>
---
 client/src/components/Workflow/Editor/Options.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/src/components/Workflow/Editor/Options.vue b/client/src/components/Workflow/Editor/Options.vue
index 8ce5effe8ea5..c08ac5063a90 100644
--- a/client/src/components/Workflow/Editor/Options.vue
+++ b/client/src/components/Workflow/Editor/Options.vue
@@ -9,6 +9,7 @@ const emit = defineEmits<{
     (e: "onReport"): void;
     (e: "onSaveAs"): void;
     (e: "onLayout"): void;
+    (e: "onLint"): void;
     (e: "onUpgrade"): void;
     (e: "onDownload"): void;
     (e: "onRun"): void;

From e10320ce5d343e12fca647de834bc2b3580ee9de Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Sun, 19 Mar 2023 20:52:18 -0700
Subject: [PATCH 19/26] add security checks to page and visualization APIs

---
 lib/galaxy/webapps/galaxy/controllers/page.py          | 4 +++-
 lib/galaxy/webapps/galaxy/controllers/visualization.py | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py
index 1c6e9c749603..a573d871b546 100644
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -377,8 +377,9 @@ def list(self, trans, *args, **kwargs):
             operation = kwargs["operation"].lower()
             ids = util.listify(kwargs["id"])
             for id in ids:
-                item = session.query(model.Page).get(self.decode_id(id))
                 if operation == "delete":
+                    item = session.query(model.Page).get(self.decode_id(id))
+                    self.security_check(trans, item, check_ownership=True)
                     item.deleted = True
             session.flush()
 
@@ -485,6 +486,7 @@ def edit(self, trans, payload=None, **kwd):
         decoded_id = self.decode_id(id)
         user = trans.get_user()
         p = trans.sa_session.query(model.Page).get(decoded_id)
+        p = self.security_check(trans, p, check_ownership=True)
         if trans.request.method == "GET":
             if p.slug is None:
                 self.slug_builder.create_item_slug(trans.sa_session, p)
diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py
index 0c6b451f2133..dc2a49ead08c 100644
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -358,8 +358,8 @@ def list(self, trans, **kwargs):
             operation = kwargs["operation"].lower()
             ids = util.listify(kwargs["id"])
             for id in ids:
-                item = session.query(model.Visualization).get(self.decode_id(id))
                 if operation == "delete":
+                    item = self.get_visualization(trans, id)
                     item.deleted = True
                 if operation == "copy":
                     self.copy(trans, **kwargs)
@@ -400,7 +400,7 @@ def index(self, trans, *args, **kwargs):
     @web.expose
     @web.require_login()
     def copy(self, trans, id, **kwargs):
-        visualization = self.get_visualization(trans, id, check_ownership=False)
+        visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
         user = trans.get_user()
         owner = visualization.user == user
         new_title = f"Copy of '{visualization.title}'"
@@ -463,7 +463,7 @@ def imp(self, trans, id):
 
         # Do import.
         session = trans.sa_session
-        visualization = self.get_visualization(trans, id, check_ownership=False)
+        visualization = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
         if visualization.importable is False:
             return trans.show_error_message(
                 f"The owner of this visualization has disabled imports via this link.<br>You can {referer_message}",

From 9ea74b65379a9d3cfb405b5cb0a2a4ed806d525b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 20 Mar 2023 11:43:07 -0400
Subject: [PATCH 20/26] Fix API for latest FastAPI (0.95).

xref https://fastapi.tiangolo.com/release-notes/
---
 client/src/schema/schema.ts                   | 140 +++---
 lib/galaxy/webapps/galaxy/api/datasets.py     | 138 ++++--
 lib/galaxy/webapps/galaxy/api/histories.py    |   1 -
 .../webapps/galaxy/api/history_contents.py    | 444 +++++++++++++-----
 4 files changed, 505 insertions(+), 218 deletions(-)

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index 7ef1e8b8ebed..e17594070cc6 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -73,7 +73,7 @@ export interface paths {
          * @description Download the content of a history dataset collection as a `zip` archive
          * while maintaining approximate collection structure.
          */
-        get: operations["download_dataset_collection_api_dataset_collections__id__download_get"];
+        get: operations["dataset_collections__download"];
     };
     "/api/dataset_collections/{id}/prepare_download": {
         /**
@@ -163,7 +163,7 @@ export interface paths {
     };
     "/api/datasets/{history_content_id}/metadata_file": {
         /** Returns the metadata file associated with this history item. */
-        get: operations["get_metadata_file_api_datasets__history_content_id__metadata_file_get"];
+        get: operations["datasets__get_metadata_file"];
     };
     "/api/datatypes": {
         /**
@@ -436,7 +436,7 @@ export interface paths {
          *
          * **Note**: Anonymous users are allowed to get their current history contents.
          */
-        get: operations["history_contents_api_histories__history_id__contents_get"];
+        get: operations["history_contents__index"];
         /**
          * Batch update specific properties of a set items contained in the given History.
          * @description Batch update specific properties of a set items contained in the given History.
@@ -450,7 +450,7 @@ export interface paths {
          * @deprecated
          * @description Create a new `HDA` or `HDCA` in the given History.
          */
-        post: operations["create_api_histories__history_id__contents_post"];
+        post: operations["history_contents__create"];
     };
     "/api/histories/{history_id}/contents/archive": {
         /**
@@ -485,7 +485,7 @@ export interface paths {
          * @description Download the content of a history dataset collection as a `zip` archive
          * while maintaining approximate collection structure.
          */
-        get: operations["download_dataset_collection_api_histories__history_id__contents_dataset_collections__id__download_get"];
+        get: operations["history_contents__download_collection"];
     };
     "/api/histories/{history_id}/contents/datasets/{id}/materialize": {
         /** Materialize a deferred dataset into real, usable dataset. */
@@ -516,7 +516,7 @@ export interface paths {
     };
     "/api/histories/{history_id}/contents/{history_content_id}/metadata_file": {
         /** Returns the metadata file associated with this history item. */
-        get: operations["get_metadata_file_api_histories__history_id__contents__history_content_id__metadata_file_get"];
+        get: operations["history_contents__get_metadata_file"];
     };
     "/api/histories/{history_id}/contents/{id}": {
         /**
@@ -526,20 +526,20 @@ export interface paths {
          *
          * **Note**: Anonymous users are allowed to get their current history contents.
          */
-        get: operations["history_content_api_histories__history_id__contents__id__get"];
+        get: operations["history_contents__show_legacy"];
         /**
-         * Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
+         * Updates the values for the history content item with the given ``ID`` and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
          * @deprecated
          * @description Updates the values for the history content item with the given ``ID``.
          */
-        put: operations["update_api_histories__history_id__contents__id__put"];
+        put: operations["history_contents__update_legacy"];
         /**
          * Delete the history dataset with the given ``ID``.
-         * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset).
+         * @description Delete the history content with the given ``ID`` and query specified type (defaults to dataset).
          *
          * **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
-        delete: operations["delete_api_histories__history_id__contents__id__delete"];
+        delete: operations["history_contents__delete_legacy"];
     };
     "/api/histories/{history_id}/contents/{id}/validate": {
         /**
@@ -551,19 +551,19 @@ export interface paths {
     "/api/histories/{history_id}/contents/{type}s": {
         /**
          * Returns the contents of the given history filtered by type.
-         * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
+         * @description Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
          *
          * - The contents can be filtered and queried using the appropriate parameters.
          * - The amount of information returned for each item can be customized.
          *
          * **Note**: Anonymous users are allowed to get their current history contents.
          */
-        get: operations["index_api_histories__history_id__contents__type_s_get"];
+        get: operations["history_contents__index_typed"];
         /**
          * Create a new `HDA` or `HDCA` in the given History.
          * @description Create a new `HDA` or `HDCA` in the given History.
          */
-        post: operations["create_api_histories__history_id__contents__type_s_post"];
+        post: operations["history_contents__create_typed"];
     };
     "/api/histories/{history_id}/contents/{type}s/{id}": {
         /**
@@ -572,19 +572,19 @@ export interface paths {
          *
          * **Note**: Anonymous users are allowed to get their current history contents.
          */
-        get: operations["history_content_typed_api_histories__history_id__contents__type_s__id__get"];
+        get: operations["history_contents__show"];
         /**
-         * Updates the values for the history content item with the given ``ID``.
+         * Updates the values for the history content item with the given ``ID`` and path specified type.
          * @description Updates the values for the history content item with the given ``ID``.
          */
-        put: operations["update_api_histories__history_id__contents__type_s__id__put"];
+        put: operations["history_contents__update_typed"];
         /**
-         * Delete the history content with the given ``ID`` and specified type.
-         * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset).
+         * Delete the history content with the given ``ID`` and path specified type.
+         * @description Delete the history content with the given ``ID`` and path specified type.
          *
          * **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
-        delete: operations["delete_api_histories__history_id__contents__type_s__id__delete"];
+        delete: operations["history_contents__delete_typed"];
     };
     "/api/histories/{history_id}/contents/{type}s/{id}/jobs_summary": {
         /**
@@ -7701,17 +7701,13 @@ export interface operations {
             };
         };
     };
-    download_dataset_collection_api_dataset_collections__id__download_get: {
+    dataset_collections__download: {
         /**
          * Download the content of a dataset collection as a `zip` archive.
          * @description Download the content of a history dataset collection as a `zip` archive
          * while maintaining approximate collection structure.
          */
         parameters: {
-            /** @description The encoded database identifier of the History. */
-            query?: {
-                history_id?: string;
-            };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
             header?: {
                 "run-as"?: string;
@@ -8174,13 +8170,11 @@ export interface operations {
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         parameters: {
-            /** @description The encoded database identifier of the History. */
             /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description TODO */
+            /** @description If non-null, get the specified filename from the extra files for this dataset. */
             /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
             /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
             query?: {
-                history_id?: string;
                 preview?: boolean;
                 filename?: string;
                 to_ext?: string;
@@ -8212,13 +8206,11 @@ export interface operations {
          * @description Streams the dataset for download or the contents preview to be displayed in a browser.
          */
         parameters: {
-            /** @description The encoded database identifier of the History. */
             /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description TODO */
+            /** @description If non-null, get the specified filename from the extra files for this dataset. */
             /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
             /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
             query?: {
-                history_id?: string;
                 preview?: boolean;
                 filename?: string;
                 to_ext?: string;
@@ -8248,13 +8240,11 @@ export interface operations {
             };
         };
     };
-    get_metadata_file_api_datasets__history_content_id__metadata_file_get: {
+    datasets__get_metadata_file: {
         /** Returns the metadata file associated with this history item. */
         parameters: {
-            /** @description The encoded database identifier of the History. */
             /** @description The name of the metadata file to retrieve. */
             query: {
-                history_id?: string;
                 metadata_file: string;
             };
             /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
@@ -9850,7 +9840,7 @@ export interface operations {
             };
         };
     };
-    history_contents_api_histories__history_id__contents_get: {
+    history_contents__index: {
         /**
          * Returns the contents of the given history.
          * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
@@ -9985,7 +9975,7 @@ export interface operations {
             };
         };
     };
-    create_api_histories__history_id__contents_post: {
+    history_contents__create: {
         /**
          * Create a new `HDA` or `HDCA` in the given History.
          * @deprecated
@@ -9993,7 +9983,7 @@ export interface operations {
          */
         parameters: {
             /**
-             * @description The type of the history element to create.
+             * @description The type of the target history element.
              * @example dataset
              */
             /** @description View to be passed to the serializer */
@@ -10212,7 +10202,7 @@ export interface operations {
             };
         };
     };
-    download_dataset_collection_api_histories__history_id__contents_dataset_collections__id__download_get: {
+    history_contents__download_collection: {
         /**
          * Download the content of a dataset collection as a `zip` archive.
          * @description Download the content of a history dataset collection as a `zip` archive
@@ -10223,6 +10213,7 @@ export interface operations {
             header?: {
                 "run-as"?: string;
             };
+            /** @description The encoded database identifier of the History. */
             /** @description The ID of the `HDCA` contained in the history. */
             path: {
                 history_id: string;
@@ -10321,7 +10312,7 @@ export interface operations {
          */
         parameters: {
             /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description TODO */
+            /** @description If non-null, get the specified filename from the extra files for this dataset. */
             /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
             /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
             query?: {
@@ -10334,6 +10325,7 @@ export interface operations {
             header?: {
                 "run-as"?: string;
             };
+            /** @description The encoded database identifier of the History. */
             /** @description The encoded database identifier of the dataset. */
             path: {
                 history_id: string;
@@ -10358,7 +10350,7 @@ export interface operations {
          */
         parameters: {
             /** @description Whether to get preview contents to be directly displayed on the web. If preview is False (default) the contents will be downloaded instead. */
-            /** @description TODO */
+            /** @description If non-null, get the specified filename from the extra files for this dataset. */
             /** @description The file extension when downloading the display data. Use the value `data` to let the server infer it from the data type. */
             /** @description The query parameter 'raw' should be considered experimental and may be dropped at some point in the future without warning. Generally, data should be processed by its datatype prior to display. */
             query?: {
@@ -10371,6 +10363,7 @@ export interface operations {
             header?: {
                 "run-as"?: string;
             };
+            /** @description The encoded database identifier of the History. */
             /** @description The encoded database identifier of the dataset. */
             path: {
                 history_id: string;
@@ -10421,7 +10414,7 @@ export interface operations {
             };
         };
     };
-    get_metadata_file_api_histories__history_id__contents__history_content_id__metadata_file_get: {
+    history_contents__get_metadata_file: {
         /** Returns the metadata file associated with this history item. */
         parameters: {
             /** @description The name of the metadata file to retrieve. */
@@ -10432,6 +10425,7 @@ export interface operations {
             header?: {
                 "run-as"?: string;
             };
+            /** @description The encoded database identifier of the History. */
             /** @description The encoded database identifier of the dataset. */
             path: {
                 history_id: string;
@@ -10449,7 +10443,7 @@ export interface operations {
             };
         };
     };
-    history_content_api_histories__history_id__contents__id__get: {
+    history_contents__show_legacy: {
         /**
          * Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
          * @deprecated
@@ -10459,7 +10453,7 @@ export interface operations {
          */
         parameters: {
             /**
-             * @description The type of the history element to show.
+             * @description The type of the target history element.
              * @example dataset
              */
             /** @description This value can be used to broadly restrict the magnitude of the number of elements returned via the API for large collections. The number of actual elements returned may be "a bit" more than this number or "a lot" less - varying on the depth of nesting, balance of nesting at each level, and size of target collection. The consumer of this API should not expect a stable number or pre-calculable number of elements to be produced given this parameter - the only promise is that this API will not respond with an order of magnitude more elements estimated with this value. The UI uses this parameter to fetch a "balanced" concept of the "start" of large collections at every depth of the collection. */
@@ -10502,15 +10496,15 @@ export interface operations {
             };
         };
     };
-    update_api_histories__history_id__contents__id__put: {
+    history_contents__update_legacy: {
         /**
-         * Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
+         * Updates the values for the history content item with the given ``ID`` and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.
          * @deprecated
          * @description Updates the values for the history content item with the given ``ID``.
          */
         parameters: {
             /**
-             * @description The type of the history element to show.
+             * @description The type of the target history element.
              * @example dataset
              */
             /** @description View to be passed to the serializer */
@@ -10556,16 +10550,16 @@ export interface operations {
             };
         };
     };
-    delete_api_histories__history_id__contents__id__delete: {
+    history_contents__delete_legacy: {
         /**
          * Delete the history dataset with the given ``ID``.
-         * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset).
+         * @description Delete the history content with the given ``ID`` and query specified type (defaults to dataset).
          *
          * **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
         parameters: {
             /**
-             * @description The type of the history element to show.
+             * @description The type of the target history element.
              * @example dataset
              */
             /**
@@ -10659,10 +10653,10 @@ export interface operations {
             };
         };
     };
-    index_api_histories__history_id__contents__type_s_get: {
+    history_contents__index_typed: {
         /**
          * Returns the contents of the given history filtered by type.
-         * @description Return a list of `HDA`/`HDCA` data for the history with the given ``ID``.
+         * @description Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
          *
          * - The contents can be filtered and queried using the appropriate parameters.
          * - The amount of information returned for each item can be customized.
@@ -10732,7 +10726,7 @@ export interface operations {
             /** @description The ID of the History. */
             path: {
                 history_id: string;
-                type: string;
+                type: components["schemas"]["HistoryContentType"];
             };
         };
         responses: {
@@ -10752,7 +10746,7 @@ export interface operations {
             };
         };
     };
-    create_api_histories__history_id__contents__type_s_post: {
+    history_contents__create_typed: {
         /**
          * Create a new `HDA` or `HDCA` in the given History.
          * @description Create a new `HDA` or `HDCA` in the given History.
@@ -10769,6 +10763,10 @@ export interface operations {
                 "run-as"?: string;
             };
             /** @description The ID of the History. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 type: components["schemas"]["HistoryContentType"];
@@ -10806,7 +10804,7 @@ export interface operations {
             };
         };
     };
-    history_content_typed_api_histories__history_id__contents__type_s__id__get: {
+    history_contents__show: {
         /**
          * Return detailed information about a specific HDA or HDCA with the given `ID` within a history.
          * @description Return detailed information about an `HDA` or `HDCA` within a history.
@@ -10828,6 +10826,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
@@ -10854,9 +10856,9 @@ export interface operations {
             };
         };
     };
-    update_api_histories__history_id__contents__type_s__id__put: {
+    history_contents__update_typed: {
         /**
-         * Updates the values for the history content item with the given ``ID``.
+         * Updates the values for the history content item with the given ``ID`` and path specified type.
          * @description Updates the values for the history content item with the given ``ID``.
          */
         parameters: {
@@ -10872,6 +10874,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
@@ -10903,10 +10909,10 @@ export interface operations {
             };
         };
     };
-    delete_api_histories__history_id__contents__type_s__id__delete: {
+    history_contents__delete_typed: {
         /**
-         * Delete the history content with the given ``ID`` and specified type.
-         * @description Delete the history content with the given ``ID`` and specified type (defaults to dataset).
+         * Delete the history content with the given ``ID`` and path specified type.
+         * @description Delete the history content with the given ``ID`` and path specified type.
          *
          * **Note**: Currently does not stop any active jobs for which this dataset is an output.
          */
@@ -10938,6 +10944,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
@@ -10987,6 +10997,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
@@ -11020,6 +11034,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
@@ -11055,6 +11073,10 @@ export interface operations {
             };
             /** @description The ID of the History. */
             /** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 id: string;
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index bba89747c79a..daa90ff9bca2 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -74,6 +74,36 @@
     description="Whether this dataset belongs to a history (HDA) or a library (LDDA).",
 )
 
+PreviewQueryParam = Query(
+    default=False,
+    description=(
+        "Whether to get preview contents to be directly displayed on the web. "
+        "If preview is False (default) the contents will be downloaded instead."
+    ),
+)
+
+FilenameQueryParam = Query(
+    default=None,
+    description="If non-null, get the specified filename from the extra files for this dataset.",
+)
+
+ToExtQueryParam = Query(
+    default=None,
+    description=(
+        "The file extension when downloading the display data. Use the value `data` to "
+        "let the server infer it from the data type."
+    ),
+)
+
+RawQueryParam = Query(
+    default=False,
+    description=(
+        "The query parameter 'raw' should be considered experimental and may be dropped at "
+        "some point in the future without warning. Generally, data should be processed by its "
+        "datatype prior to display."
+    ),
+)
+
 
 @router.cbv
 class FastAPIDatasets:
@@ -199,11 +229,6 @@ def extra_files(
     ):
         return self.service.extra_files(trans, history_content_id)
 
-    @router.get(
-        "/api/datasets/{history_content_id}/display",
-        summary="Displays (preview) or downloads dataset content.",
-        response_class=StreamingResponse,
-    )
     @router.get(
         "/api/histories/{history_id}/contents/{history_content_id}/display",
         name="history_contents_display",
@@ -211,53 +236,60 @@ def extra_files(
         tags=["histories"],
         response_class=StreamingResponse,
     )
-    @router.head(
-        "/api/datasets/{history_content_id}/display",
-        summary="Check if dataset content can be previewed or downloaded.",
-    )
     @router.head(
         "/api/histories/{history_id}/contents/{history_content_id}/display",
         name="history_contents_display",
         summary="Check if dataset content can be previewed or downloaded.",
         tags=["histories"],
     )
-    def display(
+    def display_history_content(
         self,
         request: Request,
         trans=DependsOnTrans,
-        history_id: Optional[DecodedDatabaseIdField] = Query(
-            default=None,
+        history_id: Optional[DecodedDatabaseIdField] = Path(
             description="The encoded database identifier of the History.",
         ),
         history_content_id: DecodedDatabaseIdField = DatasetIDPathParam,
-        preview: bool = Query(
-            default=False,
-            description=(
-                "Whether to get preview contents to be directly displayed on the web. "
-                "If preview is False (default) the contents will be downloaded instead."
-            ),
-        ),
-        filename: Optional[str] = Query(
-            default=None,
-            description="TODO",
-        ),
-        to_ext: Optional[str] = Query(
-            default=None,
-            description=(
-                "The file extension when downloading the display data. Use the value `data` to "
-                "let the server infer it from the data type."
-            ),
-        ),
-        raw: bool = Query(
-            default=False,
-            description=(
-                "The query parameter 'raw' should be considered experimental and may be dropped at "
-                "some point in the future without warning. Generally, data should be processed by its "
-                "datatype prior to display."
-            ),
-        ),
+        preview: bool = PreviewQueryParam,
+        filename: Optional[str] = FilenameQueryParam,
+        to_ext: Optional[str] = ToExtQueryParam,
+        raw: bool = RawQueryParam,
+    ):
+        """Streams the dataset for download or the contents preview to be displayed in a browser."""
+        return self._display(request, trans, history_content_id, preview, filename, to_ext, raw)
+
+    @router.get(
+        "/api/datasets/{history_content_id}/display",
+        summary="Displays (preview) or downloads dataset content.",
+        response_class=StreamingResponse,
+    )
+    @router.head(
+        "/api/datasets/{history_content_id}/display",
+        summary="Check if dataset content can be previewed or downloaded.",
+    )
+    def display(
+        self,
+        request: Request,
+        trans=DependsOnTrans,
+        history_content_id: DecodedDatabaseIdField = DatasetIDPathParam,
+        preview: bool = PreviewQueryParam,
+        filename: Optional[str] = FilenameQueryParam,
+        to_ext: Optional[str] = ToExtQueryParam,
+        raw: bool = RawQueryParam,
     ):
         """Streams the dataset for download or the contents preview to be displayed in a browser."""
+        return self._display(request, trans, history_content_id, preview, filename, to_ext, raw)
+
+    def _display(
+        self,
+        request: Request,
+        trans,
+        history_content_id: DecodedDatabaseIdField,
+        preview: bool,
+        filename: Optional[str],
+        to_ext: Optional[str],
+        raw: bool,
+    ):
         extra_params = get_query_parameters_from_request_excluding(
             request, {"preview", "filename", "to_ext", "raw", "dataset"}
         )
@@ -278,26 +310,46 @@ def display(
         "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
         summary="Returns the metadata file associated with this history item.",
         tags=["histories"],
+        operation_id="history_contents__get_metadata_file",
         response_class=GalaxyFileResponse,
     )
+    def get_metadata_file_history_content(
+        self,
+        trans=DependsOnTrans,
+        history_id: DecodedDatabaseIdField = Path(
+            description="The encoded database identifier of the History.",
+        ),
+        history_content_id: DecodedDatabaseIdField = DatasetIDPathParam,
+        metadata_file: str = Query(
+            ...,
+            description="The name of the metadata file to retrieve.",
+        ),
+    ):
+        return self._get_metadata_file(trans, history_content_id, metadata_file)
+
     @router.get(
         "/api/datasets/{history_content_id}/metadata_file",
         summary="Returns the metadata file associated with this history item.",
         response_class=GalaxyFileResponse,
+        operation_id="datasets__get_metadata_file",
     )
-    def get_metadata_file(
+    def get_metadata_file_datasets(
         self,
         trans=DependsOnTrans,
-        history_id: Optional[DecodedDatabaseIdField] = Query(
-            default=None,
-            description="The encoded database identifier of the History.",
-        ),
         history_content_id: DecodedDatabaseIdField = DatasetIDPathParam,
         metadata_file: str = Query(
             ...,
             description="The name of the metadata file to retrieve.",
         ),
     ):
+        return self._get_metadata_file(trans, history_content_id, metadata_file)
+
+    def _get_metadata_file(
+        self,
+        trans,
+        history_content_id: DecodedDatabaseIdField,
+        metadata_file: str,
+    ) -> GalaxyFileResponse:
         metadata_file_path, headers = self.service.get_metadata_file(trans, history_content_id, metadata_file)
         return GalaxyFileResponse(path=cast(str, metadata_file_path), headers=headers)
 
diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py
index 372ceade205a..3b32a4f080c1 100644
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -77,7 +77,6 @@
 )
 
 JehaIDPathParam: Union[DecodedDatabaseIdField, LatestLiteral] = Path(
-    default="latest",
     title="Job Export History ID",
     description=(
         "The ID of the specific Job Export History Association or "
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index add89f3c1981..9c45d9d1f903 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -92,12 +92,60 @@
 )
 
 ContentTypeQueryParam = Query(
-    default=HistoryContentType.dataset,
+    default=None,
     title="Content Type",
-    description="The type of the history element to show.",
+    description="The type of the target history element.",
     example=HistoryContentType.dataset,
 )
 
+ContentTypePathParam = Path(
+    title="Content Type",
+    description="The type of the target history element.",
+    example=HistoryContentType.dataset,
+)
+
+FuzzyCountQueryParam = Query(
+    default=None,
+    title="Fuzzy Count",
+    description=(
+        "This value can be used to broadly restrict the magnitude "
+        "of the number of elements returned via the API for large "
+        "collections. The number of actual elements returned may "
+        'be "a bit" more than this number or "a lot" less - varying '
+        "on the depth of nesting, balance of nesting at each level, "
+        "and size of target collection. The consumer of this API should "
+        "not expect a stable number or pre-calculable number of "
+        "elements to be produced given this parameter - the only "
+        "promise is that this API will not respond with an order "
+        "of magnitude more elements estimated with this value. "
+        'The UI uses this parameter to fetch a "balanced" concept of '
+        'the "start" of large collections at every depth of the '
+        "collection."
+    ),
+)
+
+PurgeQueryParam = Query(
+    default=False,
+    title="Purge",
+    description="Whether to remove from disk the target HDA or child HDAs of the target HDCA.",
+    deprecated=True,
+)
+
+RecursiveQueryParam = Query(
+    default=False,
+    title="Recursive",
+    description="When deleting a dataset collection, whether to also delete containing datasets.",
+    deprecated=True,
+)
+
+StopJobQueryParam = Query(
+    default=False,
+    title="Stop Job",
+    description="Whether to stop the creating job if all outputs of the job have been deleted.",
+    deprecated=True,
+)
+
+
 CONTENT_DELETE_RESPONSES = {
     200: {
         "description": "Request has been executed.",
@@ -155,55 +203,76 @@ def parse_index_query_params(
         raise validation_error_to_message_exception(e)
 
 
-def get_legacy_index_query_params(
-    ids: Optional[str] = Query(
-        default=None,
-        title="IDs",
-        description=(
-            "A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the "
-            "specific datasets will be returned. Also, setting this value will return `all` details of the content item."
-        ),
-        deprecated=True,
-    ),
-    types: Optional[List[str]] = Query(
-        default=None,
-        title="Types",
-        description=(
-            "A list or comma-separated list of kinds of contents to return "
-            "(currently just `dataset` and `dataset_collection` are available). "
-            "If unset, all types will be returned."
-        ),
-        deprecated=True,
+LegacyIdsQueryParam = Query(
+    default=None,
+    title="IDs",
+    description=(
+        "A comma-separated list of encoded `HDA/HDCA` IDs. If this list is provided, only information about the "
+        "specific datasets will be returned. Also, setting this value will return `all` details of the content item."
     ),
-    type: Optional[str] = Query(
-        default=None,
-        include_in_schema=False,
-        deprecated=True,
-    ),
-    details: Optional[str] = Query(
-        default=None,
-        title="Details",
-        description=("Legacy name for the `dataset_details` parameter."),
-        deprecated=True,
-    ),
-    deleted: Optional[bool] = Query(
-        default=None,
-        title="Deleted",
-        description="Whether to return deleted or undeleted datasets only. Leave unset for both.",
-        deprecated=True,
-    ),
-    visible: Optional[bool] = Query(
-        default=None,
-        title="Visible",
-        description="Whether to return visible or hidden datasets only. Leave unset for both.",
-        deprecated=True,
+    deprecated=True,
+)
+
+LegacyTypesQueryParam = Query(
+    default=None,
+    title="Types",
+    description=(
+        "A list or comma-separated list of kinds of contents to return "
+        "(currently just `dataset` and `dataset_collection` are available). "
+        "If unset, all types will be returned."
     ),
+    deprecated=True,
+)
+
+LegacyDetailsQueryParam = Query(
+    default=None,
+    title="Details",
+    description=("Legacy name for the `dataset_details` parameter."),
+    deprecated=True,
+)
+
+LegacyDeletedQueryParam = Query(
+    default=None,
+    title="Deleted",
+    description="Whether to return deleted or undeleted datasets only. Leave unset for both.",
+    deprecated=True,
+)
+
+LegacyVisibleQueryParam = Query(
+    default=None,
+    title="Visible",
+    description="Whether to return visible or hidden datasets only. Leave unset for both.",
+    deprecated=True,
+)
+
+ArchiveFilenamePathParam = Query(
+    default=None,
+    description="The name that the Archive will have (defaults to history name).",
+)
+
+ArchiveFilenameQueryParam = Query(
+    default=None,
+    description="The name that the Archive will have (defaults to history name).",
+)
+
+DryRunQueryParam = Query(
+    default=True,
+    description="Whether to return the archive and file paths only (as JSON) and not an actual archive file.",
+)
+
+
+def get_legacy_index_query_params(
+    ids: Optional[str] = LegacyIdsQueryParam,
+    types: Optional[List[str]] = LegacyTypesQueryParam,
+    details: Optional[str] = LegacyDetailsQueryParam,
+    deleted: Optional[bool] = LegacyDeletedQueryParam,
+    visible: Optional[bool] = LegacyVisibleQueryParam,
 ) -> LegacyHistoryContentsIndexParams:
     """This function is meant to be used as a dependency to render the OpenAPI documentation
     correctly"""
     return parse_legacy_index_query_params(
         ids=ids,
-        types=types or type,
+        types=types or None,
         details=details,
         deleted=deleted,
         visible=visible,
@@ -302,7 +371,39 @@ class FastAPIHistoryContents:
     @router.get(
         "/api/histories/{history_id}/contents/{type}s",
         summary="Returns the contents of the given history filtered by type.",
+        operation_id="history_contents__index_typed",
     )
+    def index_typed(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        index_params: HistoryContentsIndexParams = Depends(get_index_query_params),
+        type: HistoryContentType = Path(),
+        legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
+        serialization_params: SerializationParams = Depends(query_serialization_params),
+        filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
+        accept: str = Header(default="application/json", include_in_schema=False),
+    ) -> Union[HistoryContentsResult, HistoryContentsWithStatsResult]:
+        """
+        Return a list of either `HDA`/`HDCA` data for the history with the given ``ID``.
+
+        - The contents can be filtered and queried using the appropriate parameters.
+        - The amount of information returned for each item can be customized.
+
+        **Note**: Anonymous users are allowed to get their current history contents.
+        """
+        legacy_params.types = legacy_params.types or [type]
+        items = self.service.index(
+            trans,
+            history_id,
+            index_params,
+            legacy_params,
+            serialization_params,
+            filter_query_params,
+            accept,
+        )
+        return items
+
     @router.get(
         "/api/histories/{history_id}/contents",
         name="history_contents",
@@ -324,12 +425,18 @@ class FastAPIHistoryContents:
                 },
             },
         },
+        operation_id="history_contents__index",
     )
     def index(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         index_params: HistoryContentsIndexParams = Depends(get_index_query_params),
+        type: Optional[HistoryContentType] = Query(
+            default=None,
+            include_in_schema=False,
+            deprecated=True,
+        ),
         legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
@@ -343,6 +450,10 @@ def index(
 
         **Note**: Anonymous users are allowed to get their current history contents.
         """
+        if not legacy_params.types:
+            if type is not None:
+                legacy_params.types = [type]
+
         items = self.service.index(
             trans,
             history_id,
@@ -363,7 +474,7 @@ def show_jobs_summary(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypePathParam,
     ) -> AnyJobStateSummary:
         """Return detailed information about an `HDA` or `HDCAs` jobs.
 
@@ -378,38 +489,44 @@ def show_jobs_summary(
         "/api/histories/{history_id}/contents/{type}s/{id}",
         name="history_content_typed",
         summary="Return detailed information about a specific HDA or HDCA with the given `ID` within a history.",
+        operation_id="history_contents__show",
     )
+    def show(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        id: DecodedDatabaseIdField = HistoryItemIDPathParam,
+        type: HistoryContentType = ContentTypePathParam,
+        fuzzy_count: Optional[int] = FuzzyCountQueryParam,
+        serialization_params: SerializationParams = Depends(query_serialization_params),
+    ) -> AnyHistoryContentItem:
+        """
+        Return detailed information about an `HDA` or `HDCA` within a history.
+
+        **Note**: Anonymous users are allowed to get their current history contents.
+        """
+        return self.service.show(
+            trans,
+            id=id,
+            serialization_params=serialization_params,
+            contents_type=type,
+            fuzzy_count=fuzzy_count,
+        )
+
     @router.get(
         "/api/histories/{history_id}/contents/{id}",
         name="history_content",
         summary="Return detailed information about an HDA within a history. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.",
         deprecated=True,
+        operation_id="history_contents__show_legacy",
     )
-    def show(
+    def show_legacy(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        id: DecodedDatabaseIdField = HistoryItemIDPathParam,
         type: HistoryContentType = ContentTypeQueryParam,
-        fuzzy_count: Optional[int] = Query(
-            default=None,
-            title="Fuzzy Count",
-            description=(
-                "This value can be used to broadly restrict the magnitude "
-                "of the number of elements returned via the API for large "
-                "collections. The number of actual elements returned may "
-                'be "a bit" more than this number or "a lot" less - varying '
-                "on the depth of nesting, balance of nesting at each level, "
-                "and size of target collection. The consumer of this API should "
-                "not expect a stable number or pre-calculable number of "
-                "elements to be produced given this parameter - the only "
-                "promise is that this API will not respond with an order "
-                "of magnitude more elements estimated with this value. "
-                'The UI uses this parameter to fetch a "balanced" concept of '
-                'the "start" of large collections at every depth of the '
-                "collection."
-            ),
-        ),
+        id: DecodedDatabaseIdField = HistoryItemIDPathParam,
+        fuzzy_count: Optional[int] = FuzzyCountQueryParam,
         serialization_params: SerializationParams = Depends(query_serialization_params),
     ) -> AnyHistoryContentItem:
         """
@@ -434,7 +551,7 @@ def prepare_store_download(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypePathParam,
         payload: StoreExportPayload = Body(...),
     ) -> AsyncFile:
         return self.service.prepare_store_download(
@@ -453,7 +570,7 @@ def write_store(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypePathParam,
         payload: WriteStoreToPayload = Body(...),
     ) -> AsyncTaskResultSummary:
         return self.service.write_store(
@@ -486,20 +603,32 @@ def index_jobs_summary(
         "/api/histories/{history_id}/contents/dataset_collections/{id}/download",
         summary="Download the content of a dataset collection as a `zip` archive.",
         response_class=StreamingResponse,
+        operation_id="history_contents__download_collection",
     )
+    def download_dataset_collection_history_content(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: Optional[DecodedDatabaseIdField] = Path(
+            description="The encoded database identifier of the History.",
+        ),
+        id: DecodedDatabaseIdField = HistoryHDCAIDPathParam,
+    ):
+        """Download the content of a history dataset collection as a `zip` archive
+        while maintaining approximate collection structure.
+        """
+        archive = self.service.get_dataset_collection_archive_for_download(trans, id)
+        return StreamingResponse(archive.response(), headers=archive.get_headers())
+
     @router.get(
         "/api/dataset_collections/{id}/download",
         summary="Download the content of a dataset collection as a `zip` archive.",
         response_class=StreamingResponse,
         tags=["dataset collections"],
+        operation_id="dataset_collections__download",
     )
     def download_dataset_collection(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
-        history_id: Optional[DecodedDatabaseIdField] = Query(
-            default=None,
-            description="The encoded database identifier of the History.",
-        ),
         id: DecodedDatabaseIdField = HistoryHDCAIDPathParam,
     ):
         """Download the content of a history dataset collection as a `zip` archive
@@ -538,24 +667,43 @@ def prepare_collection_download(
     @router.post(
         "/api/histories/{history_id}/contents/{type}s",
         summary="Create a new `HDA` or `HDCA` in the given History.",
+        operation_id="history_contents__create_typed",
     )
+    def create_typed(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        type: HistoryContentType = ContentTypePathParam,
+        serialization_params: SerializationParams = Depends(query_serialization_params),
+        payload: CreateHistoryContentPayload = Body(...),
+    ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
+        """Create a new `HDA` or `HDCA` in the given History."""
+        return self._create(trans, history_id, type, serialization_params, payload)
+
     @router.post(
         "/api/histories/{history_id}/contents",
         summary="Create a new `HDA` or `HDCA` in the given History.",
         deprecated=True,
+        operation_id="history_contents__create",
     )
     def create(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        type: Optional[HistoryContentType] = Query(
-            default=None,
-            title="Content Type",
-            description="The type of the history element to create.",
-            example=HistoryContentType.dataset,
-        ),
+        type: Optional[HistoryContentType] = ContentTypeQueryParam,
         serialization_params: SerializationParams = Depends(query_serialization_params),
         payload: CreateHistoryContentPayload = Body(...),
+    ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
+        """Create a new `HDA` or `HDCA` in the given History."""
+        return self._create(trans, history_id, type, serialization_params, payload)
+
+    def _create(
+        self,
+        trans: ProvidesHistoryContext,
+        history_id: DecodedDatabaseIdField,
+        type: Optional[HistoryContentType],
+        serialization_params: SerializationParams,
+        payload: CreateHistoryContentPayload,
     ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
         """Create a new `HDA` or `HDCA` in the given History."""
         payload.type = type or payload.type
@@ -631,14 +779,28 @@ def validate(
 
     @router.put(
         "/api/histories/{history_id}/contents/{type}s/{id}",
-        summary="Updates the values for the history content item with the given ``ID``.",
+        summary="Updates the values for the history content item with the given ``ID`` and path specified type.",
+        operation_id="history_contents__update_typed",
     )
+    def update_typed(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        id: DecodedDatabaseIdField = HistoryItemIDPathParam,
+        type: HistoryContentType = ContentTypePathParam,
+        serialization_params: SerializationParams = Depends(query_serialization_params),
+        payload: UpdateHistoryContentsPayload = Body(...),
+    ) -> AnyHistoryContentItem:
+        """Updates the values for the history content item with the given ``ID``."""
+        return self.service.update(trans, history_id, id, payload.dict(), serialization_params, contents_type=type)
+
     @router.put(
         "/api/histories/{history_id}/contents/{id}",
-        summary="Updates the values for the history content item with the given ``ID``. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.",
+        summary="Updates the values for the history content item with the given ``ID`` and query specified type. ``/api/histories/{history_id}/contents/{type}s/{id}`` should be used instead.",
         deprecated=True,
+        operation_id="history_contents__update_legacy",
     )
-    def update(
+    def update_legacy(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
@@ -652,15 +814,47 @@ def update(
 
     @router.delete(
         "/api/histories/{history_id}/contents/{type}s/{id}",
-        summary="Delete the history content with the given ``ID`` and specified type.",
+        summary="Delete the history content with the given ``ID`` and path specified type.",
         responses=CONTENT_DELETE_RESPONSES,
+        operation_id="history_contents__delete_typed",
     )
+    def delete_typed(
+        self,
+        response: Response,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        id: DecodedDatabaseIdField = HistoryItemIDPathParam,
+        type: HistoryContentType = ContentTypePathParam,
+        serialization_params: SerializationParams = Depends(query_serialization_params),
+        purge: Optional[bool] = PurgeQueryParam,
+        recursive: Optional[bool] = RecursiveQueryParam,
+        stop_job: Optional[bool] = StopJobQueryParam,
+        payload: DeleteHistoryContentPayload = Body(None),
+    ):
+        """
+        Delete the history content with the given ``ID`` and path specified type.
+
+        **Note**: Currently does not stop any active jobs for which this dataset is an output.
+        """
+        return self._delete(
+            response,
+            trans,
+            id,
+            type,
+            serialization_params,
+            purge,
+            recursive,
+            stop_job,
+            payload,
+        )
+
     @router.delete(
         "/api/histories/{history_id}/contents/{id}",
         summary="Delete the history dataset with the given ``ID``.",
         responses=CONTENT_DELETE_RESPONSES,
+        operation_id="history_contents__delete_legacy",
     )
-    def delete(
+    def delete_legacy(
         self,
         response: Response,
         trans: ProvidesHistoryContext = DependsOnTrans,
@@ -668,31 +862,40 @@ def delete(
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
         type: HistoryContentType = ContentTypeQueryParam,
         serialization_params: SerializationParams = Depends(query_serialization_params),
-        purge: Optional[bool] = Query(
-            default=False,
-            title="Purge",
-            description="Whether to remove from disk the target HDA or child HDAs of the target HDCA.",
-            deprecated=True,
-        ),
-        recursive: Optional[bool] = Query(
-            default=False,
-            title="Recursive",
-            description="When deleting a dataset collection, whether to also delete containing datasets.",
-            deprecated=True,
-        ),
-        stop_job: Optional[bool] = Query(
-            default=False,
-            title="Stop Job",
-            description="Whether to stop the creating job if all outputs of the job have been deleted.",
-            deprecated=True,
-        ),
+        purge: Optional[bool] = PurgeQueryParam,
+        recursive: Optional[bool] = RecursiveQueryParam,
+        stop_job: Optional[bool] = StopJobQueryParam,
         payload: DeleteHistoryContentPayload = Body(None),
     ):
         """
-        Delete the history content with the given ``ID`` and specified type (defaults to dataset).
+        Delete the history content with the given ``ID`` and query specified type (defaults to dataset).
 
         **Note**: Currently does not stop any active jobs for which this dataset is an output.
         """
+        return self._delete(
+            response,
+            trans,
+            id,
+            type,
+            serialization_params,
+            purge,
+            recursive,
+            stop_job,
+            payload,
+        )
+
+    def _delete(
+        self,
+        response: Response,
+        trans: ProvidesHistoryContext,
+        id: DecodedDatabaseIdField,
+        type: HistoryContentType,
+        serialization_params: SerializationParams,
+        purge: Optional[bool],
+        recursive: Optional[bool],
+        stop_job: Optional[bool],
+        payload: DeleteHistoryContentPayload,
+    ):
         # TODO: should we just use the default payload and deprecate the query params?
         if payload is None:
             payload = DeleteHistoryContentPayload()
@@ -714,28 +917,39 @@ def delete(
     @router.get(
         "/api/histories/{history_id}/contents/archive/{filename}.{format}",
         summary="Build and return a compressed archive of the selected history contents.",
+        operation_id="history_contents__archive_named",
     )
+    def archive_named(
+        self,
+        trans: ProvidesHistoryContext = DependsOnTrans,
+        history_id: DecodedDatabaseIdField = HistoryIDPathParam,
+        filename: Optional[str] = ArchiveFilenamePathParam,
+        format: Optional[str] = Path(
+            description="Output format of the archive.",
+            deprecated=True,  # Looks like is not really used?
+        ),
+        dry_run: Optional[bool] = DryRunQueryParam,
+        filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
+    ):
+        """Build and return a compressed archive of the selected history contents.
+
+        **Note**: this is a volatile endpoint and settings and behavior may change."""
+        archive = self.service.archive(trans, history_id, filter_query_params, filename, dry_run)
+        if isinstance(archive, HistoryContentsArchiveDryRunResult):
+            return archive
+        return StreamingResponse(archive.response(), headers=archive.get_headers())
+
     @router.get(
         "/api/histories/{history_id}/contents/archive",
         summary="Build and return a compressed archive of the selected history contents.",
+        operation_id="history_contents__archive",
     )
     def archive(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        filename: Optional[str] = Query(
-            default=None,
-            description="The name that the Archive will have (defaults to history name).",
-        ),
-        format: Optional[str] = Query(
-            default="zip",
-            description="Output format of the archive.",
-            deprecated=True,  # Looks like is not really used?
-        ),
-        dry_run: Optional[bool] = Query(
-            default=True,
-            description="Whether to return the archive and file paths only (as JSON) and not an actual archive file.",
-        ),
+        filename: Optional[str] = ArchiveFilenameQueryParam,
+        dry_run: Optional[bool] = DryRunQueryParam,
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
     ):
         """Build and return a compressed archive of the selected history contents.

From 0dd4d3f835e916f64fbfe80fb9b6e6ea0a9b786a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 23 Mar 2023 18:23:25 +0100
Subject: [PATCH 21/26] Fix content `type` and `filename` parameters

---
 client/src/schema/schema.ts                   | 22 ++++---
 .../webapps/galaxy/api/history_contents.py    | 64 ++++++++++---------
 2 files changed, 46 insertions(+), 40 deletions(-)

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
index e17594070cc6..f3ee0d887630 100644
--- a/client/src/schema/schema.ts
+++ b/client/src/schema/schema.ts
@@ -459,7 +459,7 @@ export interface paths {
          *
          * **Note**: this is a volatile endpoint and settings and behavior may change.
          */
-        get: operations["archive_api_histories__history_id__contents_archive_get"];
+        get: operations["history_contents__archive"];
     };
     "/api/histories/{history_id}/contents/archive/{filename}.{format}": {
         /**
@@ -468,7 +468,7 @@ export interface paths {
          *
          * **Note**: this is a volatile endpoint and settings and behavior may change.
          */
-        get: operations["archive_api_histories__history_id__contents_archive__filename___format__get"];
+        get: operations["history_contents__archive_named"];
     };
     "/api/histories/{history_id}/contents/bulk": {
         /**
@@ -10034,7 +10034,7 @@ export interface operations {
             };
         };
     };
-    archive_api_histories__history_id__contents_archive_get: {
+    history_contents__archive: {
         /**
          * Build and return a compressed archive of the selected history contents.
          * @description Build and return a compressed archive of the selected history contents.
@@ -10043,10 +10043,6 @@ export interface operations {
          */
         parameters: {
             /** @description The name that the Archive will have (defaults to history name). */
-            /**
-             * @deprecated
-             * @description Output format of the archive.
-             */
             /** @description Whether to return the archive and file paths only (as JSON) and not an actual archive file. */
             /**
              * @description Generally a property name to filter by followed by an (often optional) hyphen and operator string.
@@ -10064,7 +10060,6 @@ export interface operations {
              */
             query?: {
                 filename?: string;
-                format?: string;
                 dry_run?: boolean;
                 q?: string[];
                 qv?: string[];
@@ -10096,7 +10091,7 @@ export interface operations {
             };
         };
     };
-    archive_api_histories__history_id__contents_archive__filename___format__get: {
+    history_contents__archive_named: {
         /**
          * Build and return a compressed archive of the selected history contents.
          * @description Build and return a compressed archive of the selected history contents.
@@ -10132,6 +10127,11 @@ export interface operations {
                 "run-as"?: string;
             };
             /** @description The ID of the History. */
+            /** @description The name that the Archive will have (defaults to history name). */
+            /**
+             * @deprecated
+             * @description Output format of the archive.
+             */
             path: {
                 history_id: string;
                 filename: string;
@@ -10724,6 +10724,10 @@ export interface operations {
                 "run-as"?: string;
             };
             /** @description The ID of the History. */
+            /**
+             * @description The type of the target history element.
+             * @example dataset
+             */
             path: {
                 history_id: string;
                 type: components["schemas"]["HistoryContentType"];
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 9c45d9d1f903..6deec3f66493 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -91,12 +91,15 @@
     ..., title="History Dataset Collection ID", description="The ID of the `HDCA` contained in the history."
 )
 
-ContentTypeQueryParam = Query(
-    default=None,
-    title="Content Type",
-    description="The type of the target history element.",
-    example=HistoryContentType.dataset,
-)
+
+def ContentTypeQueryParam(default: Optional[HistoryContentType]):
+    return Query(
+        default=default,
+        title="Content Type",
+        description="The type of the target history element.",
+        example=HistoryContentType.dataset,
+    )
+
 
 ContentTypePathParam = Path(
     title="Content Type",
@@ -224,6 +227,7 @@ def parse_index_query_params(
     deprecated=True,
 )
 
+
 LegacyDetailsQueryParam = Query(
     default=None,
     title="Details",
@@ -245,8 +249,7 @@ def parse_index_query_params(
     deprecated=True,
 )
 
-ArchiveFilenamePathParam = Query(
-    default=None,
+ArchiveFilenamePathParam = Path(
     description="The name that the Archive will have (defaults to history name).",
 )
 
@@ -272,7 +275,7 @@ def get_legacy_index_query_params(
     correctly"""
     return parse_legacy_index_query_params(
         ids=ids,
-        types=types or None,
+        types=types,
         details=details,
         deleted=deleted,
         visible=visible,
@@ -290,12 +293,9 @@ def parse_legacy_index_query_params(
     """Parses (legacy) query parameters for the history contents `index` operation
     and returns a model containing the values in the correct type."""
     if types:
-        if isinstance(types, list) and len(types) == 1:  # Support ?types=dataset,dataset_collection
-            content_types = util.listify(types[0])
-        else:  # Support ?types=dataset&types=dataset_collection
-            content_types = util.listify(types)
+        content_types = parse_content_types(types)
     else:
-        content_types = [e.value for e in HistoryContentType]
+        content_types = [e for e in HistoryContentType]
 
     id_list = None
     if ids:
@@ -317,6 +317,14 @@ def parse_legacy_index_query_params(
         raise validation_error_to_message_exception(e)
 
 
+def parse_content_types(types: Union[List[str], str]) -> List[HistoryContentType]:
+    if isinstance(types, list) and len(types) == 1:  # Support ?types=dataset,dataset_collection
+        content_types = util.listify(types[0])
+    else:  # Support ?types=dataset&types=dataset_collection
+        content_types = util.listify(types)
+    return [HistoryContentType[content_type] for content_type in content_types]
+
+
 def parse_dataset_details(details: Optional[str]):
     """Parses the different values that the `dataset_details` parameter
     can have from a string."""
@@ -378,7 +386,7 @@ def index_typed(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         index_params: HistoryContentsIndexParams = Depends(get_index_query_params),
-        type: HistoryContentType = Path(),
+        type: HistoryContentType = ContentTypePathParam,
         legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
@@ -392,7 +400,7 @@ def index_typed(
 
         **Note**: Anonymous users are allowed to get their current history contents.
         """
-        legacy_params.types = legacy_params.types or [type]
+        legacy_params.types = [type]
         items = self.service.index(
             trans,
             history_id,
@@ -432,11 +440,7 @@ def index(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         index_params: HistoryContentsIndexParams = Depends(get_index_query_params),
-        type: Optional[HistoryContentType] = Query(
-            default=None,
-            include_in_schema=False,
-            deprecated=True,
-        ),
+        type: Optional[str] = Query(default=None, include_in_schema=False, deprecated=True),
         legacy_params: LegacyHistoryContentsIndexParams = Depends(get_legacy_index_query_params),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         filter_query_params: FilterQueryParams = Depends(get_filter_query_params),
@@ -450,10 +454,8 @@ def index(
 
         **Note**: Anonymous users are allowed to get their current history contents.
         """
-        if not legacy_params.types:
-            if type is not None:
-                legacy_params.types = [type]
-
+        if type is not None:
+            legacy_params.types = parse_content_types(type)
         items = self.service.index(
             trans,
             history_id,
@@ -524,7 +526,7 @@ def show_legacy(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypeQueryParam(default=HistoryContentType.dataset),
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
         fuzzy_count: Optional[int] = FuzzyCountQueryParam,
         serialization_params: SerializationParams = Depends(query_serialization_params),
@@ -690,7 +692,7 @@ def create(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        type: Optional[HistoryContentType] = ContentTypeQueryParam,
+        type: Optional[HistoryContentType] = ContentTypeQueryParam(default=None),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         payload: CreateHistoryContentPayload = Body(...),
     ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
@@ -805,7 +807,7 @@ def update_legacy(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypeQueryParam(default=HistoryContentType.dataset),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         payload: UpdateHistoryContentsPayload = Body(...),
     ) -> AnyHistoryContentItem:
@@ -860,7 +862,7 @@ def delete_legacy(
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
         id: DecodedDatabaseIdField = HistoryItemIDPathParam,
-        type: HistoryContentType = ContentTypeQueryParam,
+        type: HistoryContentType = ContentTypeQueryParam(default=HistoryContentType.dataset),
         serialization_params: SerializationParams = Depends(query_serialization_params),
         purge: Optional[bool] = PurgeQueryParam,
         recursive: Optional[bool] = RecursiveQueryParam,
@@ -923,8 +925,8 @@ def archive_named(
         self,
         trans: ProvidesHistoryContext = DependsOnTrans,
         history_id: DecodedDatabaseIdField = HistoryIDPathParam,
-        filename: Optional[str] = ArchiveFilenamePathParam,
-        format: Optional[str] = Path(
+        filename: str = ArchiveFilenamePathParam,
+        format: str = Path(
             description="Output format of the archive.",
             deprecated=True,  # Looks like is not really used?
         ),

From a54211b004ad6179bba754b6eb59fd033487bfa2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 24 Mar 2023 10:22:29 +0100
Subject: [PATCH 22/26] Fix `get_metadata_file` URL generation

---
 lib/galaxy/webapps/galaxy/api/datasets.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index daa90ff9bca2..90fdad813564 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -309,6 +309,7 @@ def _display(
     @router.get(
         "/api/histories/{history_id}/contents/{history_content_id}/metadata_file",
         summary="Returns the metadata file associated with this history item.",
+        name="get_metadata_file",
         tags=["histories"],
         operation_id="history_contents__get_metadata_file",
         response_class=GalaxyFileResponse,

From 190824bc47030061a4ff5a4d1a66793347a4a394 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 25 Mar 2023 17:45:42 -0400
Subject: [PATCH 23/26] Add missing filter in job query

On my instance this brings the query time down from 1.7 seconds to
0.9ms. Saturday afternoon hacking fun with John D.
---
 lib/galaxy/managers/jobs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index a32a994b6025..14788e6f688a 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -441,6 +441,7 @@ def replace_dataset_ids(path, key, value):
                     )
                     data_conditions.append(
                         and_(
+                            a.job_id == model.Job.id,
                             a.name.in_(k),
                             a.dataset_id == b.id,  # b is the HDA used for the job
                             c.dataset_id == b.dataset_id,

From 7df19975942cd4e7d312a85f49ebacf1c137f56e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 24 Mar 2023 10:22:21 -0400
Subject: [PATCH 24/26] Update Github RSA key in circle ci configuration -

xref
https://github.blog/2023-03-23-we-updated-our-rsa-ssh-host-key/
---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index c3a75d00f84f..b8d9bb466c21 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -24,7 +24,7 @@ jobs:
           command: |-
               # Add github.com to known hosts
               mkdir -p ~/.ssh
-              echo 'github.com ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAq2A7hRGmdnm9tUDbO9IDSwBK6TbQa+PXYPCPy6rbTrTtw7PHkccKrpp0yVhp5HdEIcKr6pLlVDBfOLX9QUsyCOV0wzfjIJNlGEYsdlLJizHhbn2mUjvSAHQqZETYP81eFzLQNnPHt4EVVUh7VfDESU84KezmD5QlWpXLmvU31/yMf+Se8xhHTvKSCZIFImWwoG6mbUoWf9nzpIoaSjB+weqqUUmpaaasXVal72J+UX2B+2RPW3RcT0eOzQgqlJL3RKrTJvdsjE3JEAvGq3lGHSZXy28G3skua2SmVi/w4yCE6gbODqnTWlg7+wC604ydGXA8VJiS5ap43JXiUFFAaQ==
+              echo 'github.com ssh-rsa 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
               ' >> ~/.ssh/known_hosts
 
               # Add the user ssh key and set correct perms

From 56c3463d128886b5ce7bfd0bdef24f3103ca4016 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Mon, 27 Mar 2023 11:12:51 -0700
Subject: [PATCH 25/26] for black

---
 lib/galaxy/webapps/galaxy/api/history_contents.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 087bf239dd24..6e47bfc0b508 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -271,7 +271,6 @@ def parse_index_query_params(
 
 
 def get_legacy_index_query_params(
-
     ids: Optional[str] = LegacyIdsQueryParam,
     types: Optional[List[str]] = LegacyTypesQueryParam,
     details: Optional[str] = LegacyDetailsQueryParam,

From 14138c7f5bc4aa7c6d7a50fad09b8e942ae8bca5 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Tue, 28 Mar 2023 16:24:41 -0700
Subject: [PATCH 26/26] rename var

---
 lib/galaxy/webapps/galaxy/api/history_contents.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 6e47bfc0b508..f84a7eff27e7 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -249,7 +249,7 @@ def parse_index_query_params(
     deprecated=True,
 )
 
-ShareableQueryParam = Query(
+LegacyShareableQueryParam = Query(
     default=None,
     title="Shareable",
     description="Whether to return only shareable or not shareable datasets. Leave unset for both.",
@@ -276,7 +276,7 @@ def get_legacy_index_query_params(
     details: Optional[str] = LegacyDetailsQueryParam,
     deleted: Optional[bool] = LegacyDeletedQueryParam,
     visible: Optional[bool] = LegacyVisibleQueryParam,
-    shareable: Optional[bool] = ShareableQueryParam,
+    shareable: Optional[bool] = LegacyShareableQueryParam,
 ) -> LegacyHistoryContentsIndexParams:
     """This function is meant to be used as a dependency to render the OpenAPI documentation
     correctly"""